X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=src%2Fjalview%2Fworkers%2FAlignCalcManager.java;h=08ef3a27d4ba823888c260ef3558c30f31285716;hb=115a611d005faab33f978a469578bcacbcecc112;hp=bc5e8e3fcc678951620d74a259ef3e98e4b4e6c5;hpb=478ad312d5434cda157c2aecc0fbb4600b50da74;p=jalview.git
diff --git a/src/jalview/workers/AlignCalcManager.java b/src/jalview/workers/AlignCalcManager.java
index bc5e8e3..08ef3a2 100644
--- a/src/jalview/workers/AlignCalcManager.java
+++ b/src/jalview/workers/AlignCalcManager.java
@@ -1,35 +1,81 @@
+/*
+ * 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 .
+ * 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 jalview.datamodel.AlignmentAnnotation;
+import java.util.Set;
public class AlignCalcManager implements AlignCalcManagerI
{
- private volatile List restartable = Collections
- .synchronizedList(new ArrayList());
+ /*
+ * list of registered workers
+ */
+ private volatile List restartable;
- private volatile List blackList = Collections
- .synchronizedList(new ArrayList());
+ /*
+ * types of worker _not_ to run (for example, because they have
+ * previously thrown errors)
+ */
+ private volatile List> blackList;
- /**
+ /*
* global record of calculations in progress
*/
- private volatile Map inProgress = Collections
- .synchronizedMap(new Hashtable());
+ private volatile List inProgress;
- /**
+ /*
* record of calculations pending or in progress in the current context
*/
- private volatile Map> updating = Collections
- .synchronizedMap(new Hashtable>());
+ private volatile Map, List> updating;
+
+ /*
+ * workers that have run to completion so are candidates for visual-only
+ * update of their results
+ */
+ private HashSet canUpdate;
+
+ /**
+ * Constructor
+ */
+ public AlignCalcManager()
+ {
+ restartable = Collections
+ .synchronizedList(new ArrayList());
+ blackList = Collections.synchronizedList(
+ new ArrayList>());
+ inProgress = Collections
+ .synchronizedList(new ArrayList());
+ updating = Collections.synchronizedMap(
+ new Hashtable, List>());
+ canUpdate = new HashSet();
+ }
@Override
public void notifyStart(AlignCalcWorkerI worker)
@@ -39,10 +85,8 @@ public class AlignCalcManager implements AlignCalcManagerI
List upd = updating.get(worker.getClass());
if (upd == null)
{
- updating.put(
- worker.getClass(),
- upd = Collections
- .synchronizedList(new ArrayList()));
+ updating.put(worker.getClass(), upd = Collections
+ .synchronizedList(new ArrayList()));
}
synchronized (upd)
{
@@ -51,18 +95,9 @@ public class AlignCalcManager implements AlignCalcManagerI
}
}
- @Override
- public boolean alreadyDoing(AlignCalcWorkerI worker)
- {
- synchronized (inProgress)
- {
- return inProgress.containsKey(worker.getClass());
- }
- }
-
/*
* (non-Javadoc)
- *
+ *
* @see jalview.api.AlignCalcManagerI#isPending(jalview.api.AlignCalcWorkerI)
*/
@Override
@@ -87,52 +122,30 @@ public class AlignCalcManager implements AlignCalcManagerI
}
}
- // TODO make into api method if needed ?
- public int numberLive(AlignCalcWorkerI worker)
- {
- synchronized (updating)
- {
- List 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 canUpdate = new HashSet();
-
@Override
public void workerComplete(AlignCalcWorkerI worker)
{
synchronized (inProgress)
{
-// System.err.println("Worker "+worker.getClass()+" marked as complete.");
- inProgress.remove(worker.getClass());
+ // System.err.println("Worker " + worker + " marked as complete.");
+ inProgress.remove(worker);
List upd = updating.get(worker.getClass());
if (upd != null)
{
@@ -146,7 +159,7 @@ public class AlignCalcManager implements AlignCalcManagerI
}
@Override
- public void workerCannotRun(AlignCalcWorkerI worker)
+ public void disableWorker(AlignCalcWorkerI worker)
{
synchronized (blackList)
{
@@ -154,22 +167,24 @@ 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
@@ -178,7 +193,7 @@ 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);
}
}
@@ -218,11 +233,12 @@ 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))
{
@@ -235,17 +251,20 @@ public class AlignCalcManager implements AlignCalcManagerI
for (List 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;
@@ -264,54 +283,115 @@ public class AlignCalcManager implements AlignCalcManagerI
@Override
public List getRegisteredWorkersOfClass(
- Class workerClass)
+ Class extends AlignCalcWorkerI> workerClass)
{
List workingClass = new ArrayList();
- AlignCalcWorkerI[] workers;
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)
+ public void enableWorker(AlignCalcWorkerI worker)
{
- List workers = getRegisteredWorkersOfClass(workerClass);
- if (workers == null)
+ synchronized (blackList)
{
- return false;
+ blackList.remove(worker.getClass());
}
- for (AlignCalcWorkerI worker : workers)
+ }
+
+ @Override
+ public void removeRegisteredWorkersOfClass(
+ Class extends AlignCalcWorkerI> typeToRemove)
+ {
+ List removable = new ArrayList();
+ Set toremovannot = new HashSet();
+ synchronized (restartable)
{
- if (!isPending(worker))
+ for (AlignCalcWorkerI worker : restartable)
{
- startWorker(worker);
+ if (typeToRemove.equals(worker.getClass()))
+ {
+ removable.add(worker);
+ toremovannot.add(worker);
+ }
}
- else
+ restartable.removeAll(removable);
+ }
+ synchronized (canUpdate)
+ {
+ for (AlignCalcWorkerI worker : canUpdate)
{
- System.err.println("Pending exists for " + workerClass);
+ if (typeToRemove.equals(worker.getClass()))
+ {
+ removable.add(worker);
+ toremovannot.add(worker);
+ }
}
+ canUpdate.removeAll(removable);
}
- return true;
+ // 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 workerMayRun(AlignCalcWorkerI worker)
+ public void removeWorkerForAnnotation(AlignmentAnnotation ann)
{
- synchronized (blackList)
+ /*
+ * first just find those to remove (to avoid
+ * ConcurrentModificationException)
+ */
+ List toRemove = new ArrayList();
+ for (AlignCalcWorkerI worker : restartable)
{
- if (blackList.contains(worker.getClass()))
+ if (worker.involves(ann))
{
- blackList.remove(worker.getClass());
+ 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 upd = updating.get(worker.getClass());
+ if (upd != null)
+ {
+ upd.remove(worker);
+ }
}
}
}