2 * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
3 * Copyright (C) $$Year-Rel$$ The Jalview Authors
5 * This file is part of Jalview.
7 * Jalview is free software: you can redistribute it and/or
8 * modify it under the terms of the GNU General Public License
9 * as published by the Free Software Foundation, either version 3
10 * of the License, or (at your option) any later version.
12 * Jalview is distributed in the hope that it will be useful, but
13 * WITHOUT ANY WARRANTY; without even the implied warranty
14 * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
15 * PURPOSE. See the GNU General Public License for more details.
17 * You should have received a copy of the GNU General Public License
18 * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
19 * The Jalview Authors are detailed in the 'AUTHORS' file.
21 package jalview.workers;
23 import jalview.api.AlignCalcManagerI;
24 import jalview.api.AlignCalcWorkerI;
25 import jalview.datamodel.AlignmentAnnotation;
27 import java.util.ArrayList;
28 import java.util.Collection;
29 import java.util.Collections;
30 import java.util.HashSet;
31 import java.util.Hashtable;
32 import java.util.List;
36 public class AlignCalcManager implements AlignCalcManagerI
39 * list of registered workers
41 private volatile List<AlignCalcWorkerI> restartable;
44 * types of worker _not_ to run (for example, because they have
45 * previously thrown errors)
47 private volatile List<Class<? extends AlignCalcWorkerI>> blackList;
50 * global record of calculations in progress
52 private volatile List<AlignCalcWorkerI> inProgress;
55 * record of calculations pending or in progress in the current context
57 private volatile Map<Class<? extends AlignCalcWorkerI>, List<AlignCalcWorkerI>> updating;
60 * workers that have run to completion so are candidates for visual-only
61 * update of their results
63 private HashSet<AlignCalcWorkerI> canUpdate;
68 public AlignCalcManager()
70 restartable = Collections
71 .synchronizedList(new ArrayList<AlignCalcWorkerI>());
72 blackList = Collections.synchronizedList(
73 new ArrayList<Class<? extends AlignCalcWorkerI>>());
74 inProgress = Collections
75 .synchronizedList(new ArrayList<AlignCalcWorkerI>());
76 updating = Collections.synchronizedMap(
77 new Hashtable<Class<? extends AlignCalcWorkerI>, List<AlignCalcWorkerI>>());
78 canUpdate = new HashSet<AlignCalcWorkerI>();
82 public void notifyStart(AlignCalcWorkerI worker)
84 synchronized (updating)
86 List<AlignCalcWorkerI> upd = updating.get(worker.getClass());
89 updating.put(worker.getClass(), upd = Collections
90 .synchronizedList(new ArrayList<AlignCalcWorkerI>()));
102 * @see jalview.api.AlignCalcManagerI#isPending(jalview.api.AlignCalcWorkerI)
105 public boolean isPending(AlignCalcWorkerI workingClass)
107 List<AlignCalcWorkerI> upd;
108 synchronized (updating)
110 upd = updating.get(workingClass.getClass());
127 public boolean notifyWorking(AlignCalcWorkerI worker)
129 synchronized (inProgress)
131 if (inProgress.contains(worker))
133 return false; // worker is already working, so ask caller to wait around
137 inProgress.add(worker);
144 public void workerComplete(AlignCalcWorkerI worker)
146 synchronized (inProgress)
148 // System.err.println("Worker " + worker + " marked as complete.");
149 inProgress.remove(worker);
150 List<AlignCalcWorkerI> upd = updating.get(worker.getClass());
157 canUpdate.add(worker);
163 public void disableWorker(AlignCalcWorkerI worker)
165 synchronized (blackList)
167 blackList.add(worker.getClass());
172 public boolean isDisabled(AlignCalcWorkerI worker)
174 synchronized (blackList)
176 return blackList.contains(worker.getClass());
181 public void startWorker(AlignCalcWorkerI worker)
183 if (!isDisabled(worker))
185 Thread tw = new Thread(worker);
186 tw.setName(worker.getClass().toString());
192 public boolean isWorking(AlignCalcWorkerI worker)
194 synchronized (inProgress)
195 {// System.err.println("isWorking : worker "+(worker!=null ?
196 // worker.getClass():"null")+ " "+hashCode());
197 return worker != null && inProgress.contains(worker);
202 public boolean isWorking()
204 boolean working=false;
205 synchronized (inProgress)
207 // System.err.println("isWorking "+hashCode());
208 working |= inProgress.size() > 0;
210 synchronized (updating)
212 Collection<List<AlignCalcWorkerI>> workersLists = updating.values();
213 synchronized (workersLists)
215 for (List<AlignCalcWorkerI> workers : workersLists)
219 synchronized (workers) {
220 working |= workers.size() > 0;
230 public void registerWorker(AlignCalcWorkerI worker)
232 synchronized (restartable)
234 if (!restartable.contains(worker))
236 restartable.add(worker);
243 public void restartWorkers()
245 synchronized (restartable)
247 for (AlignCalcWorkerI worker : restartable)
255 public boolean workingInvolvedWith(
256 AlignmentAnnotation alignmentAnnotation)
258 synchronized (inProgress)
260 for (AlignCalcWorkerI worker : inProgress)
262 if (worker.involves(alignmentAnnotation))
268 synchronized (updating)
270 for (List<AlignCalcWorkerI> workers : updating.values())
272 for (AlignCalcWorkerI worker : workers)
274 if (worker.involves(alignmentAnnotation))
285 public void updateAnnotationFor(
286 Class<? extends AlignCalcWorkerI> workerClass)
289 AlignCalcWorkerI[] workers;
290 synchronized (canUpdate)
292 workers = canUpdate.toArray(new AlignCalcWorkerI[0]);
294 for (AlignCalcWorkerI worker : workers)
296 if (workerClass.equals(worker.getClass()))
298 worker.updateAnnotation();
304 public List<AlignCalcWorkerI> getRegisteredWorkersOfClass(
305 Class<? extends AlignCalcWorkerI> workerClass)
307 List<AlignCalcWorkerI> workingClass = new ArrayList<AlignCalcWorkerI>();
308 synchronized (canUpdate)
310 for (AlignCalcWorkerI worker : canUpdate)
312 if (workerClass.equals(worker.getClass()))
314 workingClass.add(worker);
318 return (workingClass.size() == 0) ? null : workingClass;
322 public void enableWorker(AlignCalcWorkerI worker)
324 synchronized (blackList)
326 blackList.remove(worker.getClass());
331 public void removeRegisteredWorkersOfClass(
332 Class<? extends AlignCalcWorkerI> typeToRemove)
334 List<AlignCalcWorkerI> removable = new ArrayList<AlignCalcWorkerI>();
335 Set<AlignCalcWorkerI> toremovannot = new HashSet<AlignCalcWorkerI>();
336 synchronized (restartable)
338 for (AlignCalcWorkerI worker : restartable)
340 if (typeToRemove.equals(worker.getClass()))
342 removable.add(worker);
343 toremovannot.add(worker);
346 restartable.removeAll(removable);
348 synchronized (canUpdate)
350 for (AlignCalcWorkerI worker : canUpdate)
352 if (typeToRemove.equals(worker.getClass()))
354 removable.add(worker);
355 toremovannot.add(worker);
358 canUpdate.removeAll(removable);
360 // TODO: finish testing this extension
363 * synchronized (inProgress) { // need to kill or mark as dead any running
364 * threads... (inProgress.get(typeToRemove)); }
366 * if (workers == null) { return; } for (AlignCalcWorkerI worker : workers)
369 * if (isPending(worker)) { worker.abortAndDestroy(); startWorker(worker); }
370 * else { System.err.println("Pending exists for " + workerClass); } }
375 * Deletes the worker that update the given annotation, provided it is marked
379 public void removeWorkerForAnnotation(AlignmentAnnotation ann)
382 * first just find those to remove (to avoid
383 * ConcurrentModificationException)
385 List<AlignCalcWorkerI> toRemove = new ArrayList<AlignCalcWorkerI>();
386 for (AlignCalcWorkerI worker : restartable)
388 if (worker.involves(ann))
390 if (worker.isDeletable())
392 toRemove.add(worker);
398 * remove all references to deleted workers so any references
399 * they hold to annotation data can be garbage collected
401 for (AlignCalcWorkerI worker : toRemove)
403 restartable.remove(worker);
404 blackList.remove(worker.getClass());
405 inProgress.remove(worker);
406 canUpdate.remove(worker);
407 synchronized (updating)
409 List<AlignCalcWorkerI> upd = updating.get(worker.getClass());