X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fworkers%2FAlignCalcManager.java;h=9a3fc8df707c7759e5df06ba35b750c76e069558;hb=a83adb45bdf9554e270921b4baad94defd314b36;hp=6a2d6ee132fb05d93b11815f0957a1ed3c77f5b4;hpb=b2f9a8d7bce642ff4011bc6d49e02bb0569fbb11;p=jalview.git

diff --git a/src/jalview/workers/AlignCalcManager.java b/src/jalview/workers/AlignCalcManager.java
index 6a2d6ee..9a3fc8d 100644
--- a/src/jalview/workers/AlignCalcManager.java
+++ b/src/jalview/workers/AlignCalcManager.java
@@ -1,23 +1,30 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
- * Copyright (C) 2014 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.
  * 
  * 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.
+ * 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/>.
+ * 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.bin.Jalview;
+import jalview.datamodel.AlignmentAnnotation;
+
 import java.util.ArrayList;
 import java.util.Collections;
 import java.util.HashSet;
@@ -26,42 +33,66 @@ import java.util.List;
 import java.util.Map;
 import java.util.Set;
 
-import jalview.api.AlignCalcManagerI;
-import jalview.api.AlignCalcWorkerI;
-import jalview.datamodel.AlignmentAnnotation;
-
 public class AlignCalcManager implements AlignCalcManagerI
 {
-  private volatile List<AlignCalcWorkerI> restartable = Collections
-          .synchronizedList(new ArrayList<AlignCalcWorkerI>());
+  public static final String STARTED = "started";
 
-  private volatile List<Class> blackList = Collections
-          .synchronizedList(new ArrayList<Class>());
+  public static final String FINISHED = "finished";
 
-  /**
+  /*
+   * 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 volatile Map<Class, AlignCalcWorkerI> inProgress = Collections
-          .synchronizedMap(new Hashtable<Class, AlignCalcWorkerI>());
+  private volatile List<AlignCalcWorkerI> inProgress;
 
-  /**
+  /*
    * record of calculations pending or in progress in the current context
    */
-  private volatile Map<Class, List<AlignCalcWorkerI>> updating = Collections
-          .synchronizedMap(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<>();
+  }
 
   @Override
   public void notifyStart(AlignCalcWorkerI worker)
   {
     synchronized (updating)
     {
+      Jalview.getInstance().notifyWorker(worker, STARTED);
       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)
       {
@@ -70,15 +101,6 @@ public class AlignCalcManager implements AlignCalcManagerI
     }
   }
 
-  @Override
-  public boolean alreadyDoing(AlignCalcWorkerI worker)
-  {
-    synchronized (inProgress)
-    {
-      return inProgress.containsKey(worker.getClass());
-    }
-  }
-
   /*
    * (non-Javadoc)
    * 
@@ -106,52 +128,31 @@ public class AlignCalcManager implements AlignCalcManagerI
     }
   }
 
-  // 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
-      if (inProgress.get(worker.getClass()) != null)
+      if (inProgress.contains(worker))
       {
-        if (false)
-        {
-          System.err
-                  .println("Warning: Multiple workers are running of type "
-                          + worker.getClass());
-        }
-        return false;
+        return false; // worker is already working, so ask caller to wait around
+      }
+      else
+      {
+        inProgress.add(worker);
       }
-      inProgress.put(worker.getClass(), worker);
     }
     return true;
   }
 
-  private final HashSet<AlignCalcWorkerI> canUpdate = new HashSet<AlignCalcWorkerI>();
-
   @Override
   public void workerComplete(AlignCalcWorkerI worker)
   {
     synchronized (inProgress)
     {
-      // System.err.println("Worker "+worker.getClass()+" marked as complete.");
-      inProgress.remove(worker.getClass());
+      Jalview.getInstance().notifyWorker(worker, FINISHED);
+      // System.err.println("Worker " + worker + " marked as complete.");
+      inProgress.remove(worker);
       List<AlignCalcWorkerI> upd = updating.get(worker.getClass());
       if (upd != null)
       {
@@ -165,7 +166,7 @@ public class AlignCalcManager implements AlignCalcManagerI
   }
 
   @Override
-  public void workerCannotRun(AlignCalcWorkerI worker)
+  public void disableWorker(AlignCalcWorkerI worker)
   {
     synchronized (blackList)
     {
@@ -173,22 +174,24 @@ public class AlignCalcManager implements AlignCalcManagerI
     }
   }
 
-  public boolean isBlackListed(Class workerType)
+  @Override
+  public boolean isDisabled(AlignCalcWorkerI worker)
   {
     synchronized (blackList)
     {
-      return blackList.contains(workerType);
+      return blackList.contains(worker.getClass());
     }
   }
 
   @Override
   public void startWorker(AlignCalcWorkerI worker)
   {
-    // System.err.println("Starting "+worker.getClass());
-    // new Exception("").printStackTrace();
-    Thread tw = new Thread(worker);
-    tw.setName(worker.getClass().toString());
-    tw.start();
+    if (!isDisabled(worker))
+    {
+      Thread tw = new Thread(worker);
+      tw.setName(worker.getClass().toString());
+      tw.start();
+    }
   }
 
   @Override
@@ -197,7 +200,7 @@ public class AlignCalcManager implements AlignCalcManagerI
     synchronized (inProgress)
     {// System.err.println("isWorking : worker "+(worker!=null ?
      // worker.getClass():"null")+ " "+hashCode());
-      return worker != null && inProgress.get(worker.getClass()) == worker;
+      return worker != null && inProgress.contains(worker);
     }
   }
 
@@ -237,11 +240,12 @@ public class AlignCalcManager implements AlignCalcManagerI
   }
 
   @Override
-  public boolean workingInvolvedWith(AlignmentAnnotation alignmentAnnotation)
+  public boolean workingInvolvedWith(
+          AlignmentAnnotation alignmentAnnotation)
   {
     synchronized (inProgress)
     {
-      for (AlignCalcWorkerI worker : inProgress.values())
+      for (AlignCalcWorkerI worker : inProgress)
       {
         if (worker.involves(alignmentAnnotation))
         {
@@ -254,17 +258,20 @@ public class AlignCalcManager implements AlignCalcManagerI
       for (List<AlignCalcWorkerI> workers : updating.values())
       {
         for (AlignCalcWorkerI worker : workers)
+        {
           if (worker.involves(alignmentAnnotation))
           {
             return true;
           }
+        }
       }
     }
     return false;
   }
 
   @Override
-  public void updateAnnotationFor(Class workerClass)
+  public void updateAnnotationFor(
+          Class<? extends AlignCalcWorkerI> workerClass)
   {
 
     AlignCalcWorkerI[] workers;
@@ -283,64 +290,37 @@ public class AlignCalcManager implements AlignCalcManagerI
 
   @Override
   public List<AlignCalcWorkerI> getRegisteredWorkersOfClass(
-          Class workerClass)
+          Class<? extends AlignCalcWorkerI> workerClass)
   {
-    List<AlignCalcWorkerI> workingClass = new ArrayList<AlignCalcWorkerI>();
-    AlignCalcWorkerI[] workers;
+    List<AlignCalcWorkerI> workingClass = new ArrayList<>();
     synchronized (canUpdate)
     {
-      workers = canUpdate.toArray(new AlignCalcWorkerI[0]);
-    }
-    for (AlignCalcWorkerI worker : workers)
-    {
-      if (workerClass.equals(worker.getClass()))
+      for (AlignCalcWorkerI worker : canUpdate)
       {
-        workingClass.add(worker);
+        if (workerClass.equals(worker.getClass()))
+        {
+          workingClass.add(worker);
+        }
       }
     }
     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)
-    {
-      if (!isPending(worker))
-      {
-        startWorker(worker);
-      }
-      else
-      {
-        System.err.println("Pending exists for " + workerClass);
-      }
-    }
-    return true;
-  }
-
-  @Override
-  public void workerMayRun(AlignCalcWorkerI worker)
+  public void enableWorker(AlignCalcWorkerI worker)
   {
     synchronized (blackList)
     {
-      if (blackList.contains(worker.getClass()))
-      {
-        blackList.remove(worker.getClass());
-      }
+      blackList.remove(worker.getClass());
     }
   }
 
   @Override
-  public void removeRegisteredWorkersOfClass(Class typeToRemove)
+  public void removeRegisteredWorkersOfClass(
+          Class<? extends AlignCalcWorkerI> typeToRemove)
   {
-    List<AlignCalcWorkerI> workers = getRegisteredWorkersOfClass(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)
@@ -378,4 +358,48 @@ public class AlignCalcManager implements AlignCalcManagerI
      * 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<>();
+    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);
+        }
+      }
+    }
+  }
 }