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.Collections;
29 import java.util.HashSet;
30 import java.util.Hashtable;
31 import java.util.List;
35 public class AlignCalcManager implements AlignCalcManagerI
38 * list of registered workers
40 private volatile List<AlignCalcWorkerI> restartable;
43 * types of worker _not_ to run (for example, because they have
44 * previously thrown errors)
46 private volatile List<Class<? extends AlignCalcWorkerI>> blackList;
49 * global record of calculations in progress
51 private volatile List<AlignCalcWorkerI> inProgress;
54 * record of calculations pending or in progress in the current context
56 private volatile Map<Class<? extends AlignCalcWorkerI>, List<AlignCalcWorkerI>> updating;
59 * workers that have run to completion so are candidates for visual-only
60 * update of their results
62 private HashSet<AlignCalcWorkerI> canUpdate;
67 public AlignCalcManager()
69 restartable = Collections
70 .synchronizedList(new ArrayList<AlignCalcWorkerI>());
71 blackList = Collections
72 .synchronizedList(new ArrayList<Class<? extends AlignCalcWorkerI>>());
73 inProgress = Collections
74 .synchronizedList(new ArrayList<AlignCalcWorkerI>());
75 updating = Collections
76 .synchronizedMap(new Hashtable<Class<? extends AlignCalcWorkerI>, List<AlignCalcWorkerI>>());
77 canUpdate = new HashSet<AlignCalcWorkerI>();
81 public void notifyStart(AlignCalcWorkerI worker)
83 synchronized (updating)
85 List<AlignCalcWorkerI> upd = updating.get(worker.getClass());
91 .synchronizedList(new ArrayList<AlignCalcWorkerI>()));
103 * @see jalview.api.AlignCalcManagerI#isPending(jalview.api.AlignCalcWorkerI)
106 public boolean isPending(AlignCalcWorkerI workingClass)
108 List<AlignCalcWorkerI> upd;
109 synchronized (updating)
111 upd = updating.get(workingClass.getClass());
128 public boolean notifyWorking(AlignCalcWorkerI worker)
130 synchronized (inProgress)
132 if (inProgress.contains(worker))
134 System.err.println("Implementation error: duplicate run of worker "
139 inProgress.add(worker);
146 public void workerComplete(AlignCalcWorkerI worker)
148 synchronized (inProgress)
150 // System.err.println("Worker " + worker + " marked as complete.");
151 inProgress.remove(worker);
152 List<AlignCalcWorkerI> upd = updating.get(worker.getClass());
159 canUpdate.add(worker);
165 public void disableWorker(AlignCalcWorkerI worker)
167 synchronized (blackList)
169 blackList.add(worker.getClass());
174 public boolean isDisabled(AlignCalcWorkerI worker)
176 synchronized (blackList)
178 return blackList.contains(worker.getClass());
183 public void startWorker(AlignCalcWorkerI worker)
185 if (!isDisabled(worker))
187 Thread tw = new Thread(worker);
188 tw.setName(worker.getClass().toString());
194 public boolean isWorking(AlignCalcWorkerI worker)
196 synchronized (inProgress)
197 {// System.err.println("isWorking : worker "+(worker!=null ?
198 // worker.getClass():"null")+ " "+hashCode());
199 return worker != null && inProgress.contains(worker);
204 public boolean isWorking()
206 synchronized (inProgress)
208 // System.err.println("isWorking "+hashCode());
209 return inProgress.size() > 0;
214 public void registerWorker(AlignCalcWorkerI worker)
216 synchronized (restartable)
218 if (!restartable.contains(worker))
220 restartable.add(worker);
227 public void restartWorkers()
229 synchronized (restartable)
231 for (AlignCalcWorkerI worker : restartable)
239 public boolean workingInvolvedWith(AlignmentAnnotation alignmentAnnotation)
241 synchronized (inProgress)
243 for (AlignCalcWorkerI worker : inProgress)
245 if (worker.involves(alignmentAnnotation))
251 synchronized (updating)
253 for (List<AlignCalcWorkerI> workers : updating.values())
255 for (AlignCalcWorkerI worker : workers)
257 if (worker.involves(alignmentAnnotation))
268 public void updateAnnotationFor(
269 Class<? extends AlignCalcWorkerI> workerClass)
272 AlignCalcWorkerI[] workers;
273 synchronized (canUpdate)
275 workers = canUpdate.toArray(new AlignCalcWorkerI[0]);
277 for (AlignCalcWorkerI worker : workers)
279 if (workerClass.equals(worker.getClass()))
281 worker.updateAnnotation();
287 public List<AlignCalcWorkerI> getRegisteredWorkersOfClass(
288 Class<? extends AlignCalcWorkerI> workerClass)
290 List<AlignCalcWorkerI> workingClass = new ArrayList<AlignCalcWorkerI>();
291 synchronized (canUpdate)
293 for (AlignCalcWorkerI worker : canUpdate)
295 if (workerClass.equals(worker.getClass()))
297 workingClass.add(worker);
301 return (workingClass.size() == 0) ? null : workingClass;
305 public void enableWorker(AlignCalcWorkerI worker)
307 synchronized (blackList)
309 blackList.remove(worker.getClass());
314 public void removeRegisteredWorkersOfClass(
315 Class<? extends AlignCalcWorkerI> typeToRemove)
317 List<AlignCalcWorkerI> removable = new ArrayList<AlignCalcWorkerI>();
318 Set<AlignCalcWorkerI> toremovannot = new HashSet<AlignCalcWorkerI>();
319 synchronized (restartable)
321 for (AlignCalcWorkerI worker : restartable)
323 if (typeToRemove.equals(worker.getClass()))
325 removable.add(worker);
326 toremovannot.add(worker);
329 restartable.removeAll(removable);
331 synchronized (canUpdate)
333 for (AlignCalcWorkerI worker : canUpdate)
335 if (typeToRemove.equals(worker.getClass()))
337 removable.add(worker);
338 toremovannot.add(worker);
341 canUpdate.removeAll(removable);
343 // TODO: finish testing this extension
346 * synchronized (inProgress) { // need to kill or mark as dead any running
347 * threads... (inProgress.get(typeToRemove)); }
349 * if (workers == null) { return; } for (AlignCalcWorkerI worker : workers)
352 * if (isPending(worker)) { worker.abortAndDestroy(); startWorker(worker); }
353 * else { System.err.println("Pending exists for " + workerClass); } }
358 * Deletes the worker that update the given annotation, provided it is marked
362 public void removeWorkerForAnnotation(AlignmentAnnotation ann)
365 * first just find those to remove (to avoid
366 * ConcurrentModificationException)
368 List<AlignCalcWorkerI> toRemove = new ArrayList<AlignCalcWorkerI>();
369 for (AlignCalcWorkerI worker : restartable)
371 if (worker.involves(ann))
373 if (worker.isDeletable())
375 toRemove.add(worker);
381 * remove all references to deleted workers so any references
382 * they hold to annotation data can be garbage collected
384 for (AlignCalcWorkerI worker : toRemove)
386 restartable.remove(worker);
387 blackList.remove(worker.getClass());
388 inProgress.remove(worker);
389 canUpdate.remove(worker);
390 synchronized (updating)
392 List<AlignCalcWorkerI> upd = updating.get(worker.getClass());