package jalview.workers;
import java.util.ArrayList;
+import java.util.Collections;
import java.util.HashSet;
import java.util.Hashtable;
import java.util.List;
public class AlignCalcManager implements AlignCalcManagerI
{
- private volatile List<AlignCalcWorkerI> restartable = new ArrayList<AlignCalcWorkerI>();
+ private volatile List<AlignCalcWorkerI> restartable = Collections
+ .synchronizedList(new ArrayList<AlignCalcWorkerI>());
- private final List<Class> blackList = new ArrayList<Class>();
+ private volatile List<Class> blackList = Collections
+ .synchronizedList(new ArrayList<Class>());
/**
* global record of calculations in progress
*/
- private final 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 final 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)
+ {
+ synchronized (inProgress)
+ {
+ return inProgress.containsKey(worker.getClass());
+ }
+ }
+
+ /*
+ * (non-Javadoc)
+ *
+ * @see jalview.api.AlignCalcManagerI#isPending(jalview.api.AlignCalcWorkerI)
+ */
+ @Override
+ public boolean isPending(AlignCalcWorkerI workingClass)
+ {
+ 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)
{
- return inProgress.containsKey(worker.getClass());
+ synchronized (updating)
+ {
+ List<AlignCalcWorkerI> upd = updating.get(worker.getClass());
+ if (upd == null)
+ {
+ return 0;
+ }
+ ;
+ return upd.size();
+ }
}
@Override
- public synchronized boolean notifyWorking(AlignCalcWorkerI worker)
+ public boolean notifyWorking(AlignCalcWorkerI worker)
{
- // synchronized (inProgress)
+ synchronized (inProgress)
{
// TODO: decide if we should throw exceptions here if multiple workers
// start to work
return true;
}
- private final 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);
+ 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();
+ 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[0]))
+
+ AlignCalcWorkerI[] workers;
+ synchronized (canUpdate)
+ {
+ workers = canUpdate.toArray(new AlignCalcWorkerI[0]);
+ }
+ for (AlignCalcWorkerI worker : workers)
{
if (workerClass.equals(worker.getClass()))
{
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[0]);
+ }
+ 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());
+ }
}
}
}
super(alignViewport, alignPanel);
}
+ @Override
public void run()
{
+ if (calcMan.isPending(this))
+ {
+ return;
+ }
+ calcMan.notifyStart(this);
+ long started=System.currentTimeMillis();
try
{
AlignmentAnnotation consensus = alignViewport.getAlignmentConsensusAnnotation();
- if (consensus==null) { return;
+ if (consensus==null || calcMan.isPending(this)) {
+ calcMan.workerComplete(this);
+ return;
}
- calcMan.notifyStart(this);
- while (!calcMan.notifyWorking(this))
+ while (!calcMan.notifyWorking(this))
{
+ // System.err.println("Thread (Consensus"+Thread.currentThread().getName()+") Waiting around.");
try
{
if (ap != null)
{
- ap.paintAlignment(false);
+ ap.paintAlignment(false);
}
-
Thread.sleep(200);
} catch (Exception ex)
{
ex.printStackTrace();
}
}
- calcMan.notifyWorking(this);
if (alignViewport.isClosed())
{
abortAndDestroy();
consensus.annotations = new Annotation[aWidth];
Hashtable[] hconsensus = alignViewport.getSequenceConsensusHash();
hconsensus = new Hashtable[aWidth];
- AAFrequency.calculate(alignment.getSequencesArray(), 0,
+ try {
+ AAFrequency.calculate(alignment.getSequencesArray(), 0,
alignment.getWidth(), hconsensus, true);
+ } catch (ArrayIndexOutOfBoundsException x){
+ // this happens due to a race condition -
+ // alignment was edited at same time as calculation was running
+ //
+// calcMan.workerCannotRun(this);
+ calcMan.workerComplete(this);
+ return;
+ }
alignViewport.setSequenceConsensusHash(hconsensus);
updateResultAnnotation(true);
ColourSchemeI globalColourScheme = alignViewport
* update the consensus annotation from the sequence profile data using
* current visualization settings.
*/
+ @Override
public void updateAnnotation()
{
updateResultAnnotation(false);