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.bin.Cache;
26 import jalview.datamodel.AlignmentAnnotation;
28 import java.util.ArrayList;
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<>();
81 private static boolean listContains(List<AlignCalcWorkerI> upd,
82 AlignCalcWorkerI worker)
84 // avoid use of 'Contains' in case
85 for (AlignCalcWorkerI _otherworker : upd)
87 if (_otherworker == upd)
95 public void notifyStart(AlignCalcWorkerI worker)
97 synchronized (updating)
99 List<AlignCalcWorkerI> upd = updating.get(worker.getClass());
102 updating.put(worker.getClass(), upd = Collections
103 .synchronizedList(new ArrayList<AlignCalcWorkerI>()));
107 if (listContains(upd, worker))
110 "Ignoring second call to notifyStart for worker "
124 * @see jalview.api.AlignCalcManagerI#isPending(jalview.api.AlignCalcWorkerI)
127 public boolean isPending(AlignCalcWorkerI workingClass)
129 List<AlignCalcWorkerI> upd;
130 synchronized (updating)
132 upd = updating.get(workingClass.getClass());
149 public boolean notifyWorking(AlignCalcWorkerI worker)
151 synchronized (inProgress)
153 if (listContains(inProgress, worker))
155 return false; // worker is already working, so ask caller to wait around
159 inProgress.add(worker);
166 public void workerComplete(AlignCalcWorkerI worker)
168 synchronized (inProgress)
170 Cache.log.debug("Worker " + worker + " marked as complete.");
171 inProgress.remove(worker);
172 List<AlignCalcWorkerI> upd = updating.get(worker.getClass());
179 canUpdate.add(worker);
185 public void disableWorker(AlignCalcWorkerI worker)
187 synchronized (blackList)
189 blackList.add(worker.getClass());
194 public boolean isDisabled(AlignCalcWorkerI worker)
196 synchronized (blackList)
198 return blackList.contains(worker.getClass());
203 public void startWorker(AlignCalcWorkerI worker)
205 if (!isDisabled(worker))
207 Thread tw = new Thread(worker);
208 tw.setName(worker.getClass().toString());
214 public boolean isWorking(AlignCalcWorkerI worker)
216 synchronized (inProgress)
217 {// System.err.println("isWorking : worker "+(worker!=null ?
218 // worker.getClass():"null")+ " "+hashCode());
219 return worker != null && inProgress.contains(worker);
224 public boolean isWorking()
226 synchronized (inProgress)
228 // System.err.println("isWorking "+hashCode());
229 return inProgress.size() > 0;
234 public void registerWorker(AlignCalcWorkerI worker)
236 synchronized (restartable)
238 if (!listContains(restartable, worker))
240 restartable.add(worker);
247 public void restartWorkers()
249 synchronized (restartable)
251 for (AlignCalcWorkerI worker : restartable)
259 public boolean workingInvolvedWith(
260 AlignmentAnnotation alignmentAnnotation)
262 synchronized (inProgress)
264 for (AlignCalcWorkerI worker : inProgress)
266 if (worker.involves(alignmentAnnotation))
272 synchronized (updating)
274 for (List<AlignCalcWorkerI> workers : updating.values())
276 for (AlignCalcWorkerI worker : workers)
278 if (worker.involves(alignmentAnnotation))
289 public void updateAnnotationFor(
290 Class<? extends AlignCalcWorkerI> workerClass)
293 AlignCalcWorkerI[] workers;
294 synchronized (canUpdate)
296 workers = canUpdate.toArray(new AlignCalcWorkerI[0]);
298 for (AlignCalcWorkerI worker : workers)
300 if (workerClass.equals(worker.getClass()))
302 worker.updateAnnotation();
308 public List<AlignCalcWorkerI> getRegisteredWorkersOfClass(
309 Class<? extends AlignCalcWorkerI> workerClass)
311 List<AlignCalcWorkerI> workingClass = new ArrayList<>();
312 synchronized (canUpdate)
314 for (AlignCalcWorkerI worker : canUpdate)
316 if (workerClass.equals(worker.getClass()))
318 workingClass.add(worker);
322 return (workingClass.size() == 0) ? null : workingClass;
326 public void enableWorker(AlignCalcWorkerI worker)
328 synchronized (blackList)
330 blackList.remove(worker.getClass());
335 public void removeRegisteredWorkersOfClass(
336 Class<? extends AlignCalcWorkerI> typeToRemove)
338 List<AlignCalcWorkerI> removable = new ArrayList<>();
339 Set<AlignCalcWorkerI> toremovannot = new HashSet<>();
340 synchronized (restartable)
342 for (AlignCalcWorkerI worker : restartable)
344 if (typeToRemove.equals(worker.getClass()))
346 removable.add(worker);
347 toremovannot.add(worker);
350 restartable.removeAll(removable);
352 synchronized (canUpdate)
354 for (AlignCalcWorkerI worker : canUpdate)
356 if (typeToRemove.equals(worker.getClass()))
358 removable.add(worker);
359 toremovannot.add(worker);
362 canUpdate.removeAll(removable);
364 // TODO: finish testing this extension
367 * synchronized (inProgress) { // need to kill or mark as dead any running
368 * threads... (inProgress.get(typeToRemove)); }
370 * if (workers == null) { return; } for (AlignCalcWorkerI worker : workers)
373 * if (isPending(worker)) { worker.abortAndDestroy(); startWorker(worker); }
374 * else { System.err.println("Pending exists for " + workerClass); } }
379 * Deletes the worker that update the given annotation, provided it is marked
383 public void removeWorkerForAnnotation(AlignmentAnnotation ann)
386 * first just find those to remove (to avoid
387 * ConcurrentModificationException)
389 List<AlignCalcWorkerI> toRemove = new ArrayList<>();
390 for (AlignCalcWorkerI worker : restartable)
392 if (worker.involves(ann))
394 if (worker.isDeletable())
396 toRemove.add(worker);
402 * remove all references to deleted workers so any references
403 * they hold to annotation data can be garbage collected
405 for (AlignCalcWorkerI worker : toRemove)
407 restartable.remove(worker);
408 blackList.remove(worker.getClass());
409 inProgress.remove(worker);
410 canUpdate.remove(worker);
411 synchronized (updating)
413 List<AlignCalcWorkerI> upd = updating.get(worker.getClass());