+/*
+ * 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);
+ }
+ }
+ }
}
}
git://source.jalview.org / jalview.git / blobdiff