import jalview.api.AlignCalcManagerI;
import jalview.api.AlignCalcWorkerI;
+import jalview.bin.Cache;
import jalview.datamodel.AlignmentAnnotation;
import java.util.ArrayList;
public class AlignCalcManager implements AlignCalcManagerI
{
- private volatile List<AlignCalcWorkerI> restartable = Collections
- .synchronizedList(new ArrayList<AlignCalcWorkerI>());
+ /*
+ * list of registered workers
+ */
+ private volatile List<AlignCalcWorkerI> restartable;
- private volatile List<AlignCalcWorkerI> blackList = Collections
- .synchronizedList(new ArrayList<AlignCalcWorkerI>());
+ /*
+ * 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<>();
+ }
+
+ 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)
{
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)
{
- upd.add(worker);
+ if (listContains(upd, worker))
+ {
+ Cache.log.debug(
+ "Ignoring second call to notifyStart for worker "
+ + worker);
+ }
+ else
+ {
+ upd.add(worker);
+ }
}
}
}
- @Override
- public boolean alreadyDoing(AlignCalcWorkerI worker)
- {
- synchronized (inProgress)
- {
- return inProgress.containsKey(worker.getClass());
- }
- }
-
/*
* (non-Javadoc)
*
}
}
- // 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 (listContains(inProgress, 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());
+ Cache.log.debug("Worker " + worker + " marked as complete.");
+ inProgress.remove(worker);
List<AlignCalcWorkerI> upd = updating.get(worker.getClass());
if (upd != null)
{
{
synchronized (blackList)
{
- blackList.add(worker);
+ blackList.add(worker.getClass());
}
}
- public boolean isBlackListed(AlignCalcWorkerI worker)
+ @Override
+ public boolean isDisabled(AlignCalcWorkerI worker)
{
synchronized (blackList)
{
- return blackList.contains(worker);
+ return blackList.contains(worker.getClass());
}
}
@Override
public void startWorker(AlignCalcWorkerI worker)
{
- if (!isBlackListed(worker))
+ if (!isDisabled(worker))
{
Thread tw = new Thread(worker);
tw.setName(worker.getClass().toString());
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);
}
}
{
synchronized (restartable)
{
- if (!restartable.contains(worker))
+ if (!listContains(restartable, worker))
{
restartable.add(worker);
}
}
@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))
{
}
@Override
- public void updateAnnotationFor(Class workerClass)
+ public void updateAnnotationFor(
+ Class<? extends AlignCalcWorkerI> workerClass)
{
AlignCalcWorkerI[] workers;
@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[canUpdate.size()]);
- }
- 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 enableWorker(AlignCalcWorkerI worker)
{
synchronized (blackList)
{
- blackList.remove(worker);
+ 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)
* 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))
}
/*
- * remove all references to the workers
+ * 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);
+ 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);
+ }
+ }
}
}
}