/*******************************************************************************
* GenPlay, Einstein Genome Analyzer
* Copyright (C) 2009, 2014 Albert Einstein College of Medicine
*
* This program 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.
*
* This program 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 this program. If not, see <http://www.gnu.org/licenses/>.
* Authors: Julien Lajugie <julien.lajugie@einstein.yu.edu>
* Nicolas Fourel <nicolas.fourel@einstein.yu.edu>
* Eric Bouhassira <eric.bouhassira@einstein.yu.edu>
*
* Website: <http://genplay.einstein.yu.edu>
******************************************************************************/
package edu.yu.einstein.genplay.core.operation.SCWList;
import java.security.InvalidParameterException;
import java.util.ArrayList;
import java.util.Collection;
import java.util.concurrent.Callable;
import edu.yu.einstein.genplay.core.manager.project.ProjectChromosomes;
import edu.yu.einstein.genplay.core.manager.project.ProjectManager;
import edu.yu.einstein.genplay.core.operation.Operation;
import edu.yu.einstein.genplay.core.operationPool.OperationPool;
import edu.yu.einstein.genplay.dataStructure.chromosome.Chromosome;
import edu.yu.einstein.genplay.dataStructure.enums.SCWListType;
import edu.yu.einstein.genplay.dataStructure.list.chromosomeWideList.SCWListView.SCWListViewBuilder;
import edu.yu.einstein.genplay.dataStructure.list.chromosomeWideList.SCWListView.dense.DenseSCWListViewBuilder;
import edu.yu.einstein.genplay.dataStructure.list.chromosomeWideList.SCWListView.generic.GenericSCWListViewBuilder;
import edu.yu.einstein.genplay.dataStructure.list.chromosomeWideList.SCWListView.mask.MaskListViewBuilder;
import edu.yu.einstein.genplay.dataStructure.list.genomeWideList.GenomicListView;
import edu.yu.einstein.genplay.dataStructure.list.genomeWideList.SCWList.SCWList;
import edu.yu.einstein.genplay.dataStructure.list.genomeWideList.SCWList.SCWListBuilder;
import edu.yu.einstein.genplay.dataStructure.list.genomeWideList.SCWList.SimpleSCWList.SimpleSCWList;
import edu.yu.einstein.genplay.dataStructure.list.genomeWideList.SCWList.binList.BinList;
import edu.yu.einstein.genplay.dataStructure.list.listView.ListView;
import edu.yu.einstein.genplay.dataStructure.scoredChromosomeWindow.ScoredChromosomeWindow;
/**
* Converts a {@link GenomicListView} of objects that extends the {@link ScoredChromosomeWindow}
* interface into a {@link SimpleSCWList}.
* @author Julien Lajugie
*/
public class SCWLOConvertIntoSimpleSCWList implements Operation<SCWList> {
private final GenomicListView<? extends ScoredChromosomeWindow> inputList; // input list
private final SCWListViewBuilder lvbPrototype; // prototype of list view builder
private boolean stopped = false;// true if the operation must be stopped
/**
* Creates an instance of {@link SCWLOConvertIntoSimpleSCWList}
* @param inputList list to convert
* @param listType type of the result SCWList. Cannot be a {@link BinList}
*/
public SCWLOConvertIntoSimpleSCWList(GenomicListView<? extends ScoredChromosomeWindow> inputList, SCWListType listType) {
this.inputList = inputList;
lvbPrototype = createPrototype(listType);
}
@Override
public SCWList compute() throws Exception {
ProjectChromosomes projectChromosomes = ProjectManager.getInstance().getProjectChromosomes();
final OperationPool op = OperationPool.getInstance();
final Collection<Callable<Void>> threadList = new ArrayList<Callable<Void>>();
final SCWListBuilder resultListBuilder = new SCWListBuilder(lvbPrototype);
for (final Chromosome chromosome: projectChromosomes) {
final ListView<? extends ScoredChromosomeWindow> currentList = inputList.get(chromosome);
Callable<Void> currentThread = new Callable<Void>() {
@Override
public Void call() throws Exception {
if (currentList != null) {
for (int i = 0; (i < currentList.size()) && !stopped; i++) {
ScoredChromosomeWindow scw = currentList.get(i);
float score = scw.getScore();
if (score != 0) {
int start = scw.getStart();
int stop = scw.getStop();
resultListBuilder.addElementToBuild(chromosome, start, stop, score);
}
}
}
// tell the operation pool that a chromosome is done
op.notifyDone();
return null;
}
};
threadList.add(currentThread);
}
op.startPool(threadList);
return resultListBuilder.getSCWList();
}
/**
* @param listType a type of {@link SCWList}
* @return a SCWListViewBuilder to create the result list
*/
private SCWListViewBuilder createPrototype(SCWListType listType) {
switch (listType) {
case BIN:
throw new InvalidParameterException("This object cannot build a BinList");
case DENSE:
return new DenseSCWListViewBuilder();
case GENERIC:
return new GenericSCWListViewBuilder();
case MASK:
return new MaskListViewBuilder();
default:
break;
}
return null;
}
@Override
public String getDescription() {
return "Operation: Convert Into Gene List";
}
@Override
public String getProcessingDescription() {
return "Converting Layer";
}
@Override
public int getStepCount() {
return 1;
}
@Override
public void stop() {
stopped = true;
}
}