/*******************************************************************************
* 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.util.ArrayList;
import java.util.Collection;
import java.util.List;
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.GeneScoreType;
import edu.yu.einstein.genplay.dataStructure.enums.Strand;
import edu.yu.einstein.genplay.dataStructure.gene.Gene;
import edu.yu.einstein.genplay.dataStructure.gene.SimpleGene;
import edu.yu.einstein.genplay.dataStructure.list.chromosomeWideList.geneListView.GeneListViewBuilder;
import edu.yu.einstein.genplay.dataStructure.list.genomeWideList.ListOfListViewBuilder;
import edu.yu.einstein.genplay.dataStructure.list.genomeWideList.SCWList.SCWList;
import edu.yu.einstein.genplay.dataStructure.list.genomeWideList.geneList.GeneList;
import edu.yu.einstein.genplay.dataStructure.list.genomeWideList.geneList.SimpleGeneList;
import edu.yu.einstein.genplay.dataStructure.list.listView.ListView;
import edu.yu.einstein.genplay.dataStructure.list.listView.ListViewBuilder;
import edu.yu.einstein.genplay.dataStructure.scoredChromosomeWindow.ScoredChromosomeWindow;
import edu.yu.einstein.genplay.util.ListView.SCWListViews;
/**
* Converts a SCWList into a gene list.
* @author Julien Lajugie
*/
public class SCWLOConvertIntoGeneList implements Operation<GeneList> {
private final SCWList scwList; // input list
private boolean stopped = false;// true if the operation must be stopped
/**
* Creates an instance of {@link SCWLOConvertIntoGeneList}
* @param scwList
*/
public SCWLOConvertIntoGeneList(SCWList scwList) {
this.scwList = scwList;
}
@Override
public GeneList compute() throws Exception {
ProjectChromosomes projectChromosomes = ProjectManager.getInstance().getProjectChromosomes();
final OperationPool op = OperationPool.getInstance();
final Collection<Callable<Void>> threadList = new ArrayList<Callable<Void>>();
ListViewBuilder<Gene> lvbPrototype = new GeneListViewBuilder();
final ListOfListViewBuilder<Gene> resultListBuilder = new ListOfListViewBuilder<Gene>(lvbPrototype);
for (final Chromosome chromosome: projectChromosomes) {
final ListView<ScoredChromosomeWindow> currentList = scwList.get(chromosome);
Callable<Void> currentThread = new Callable<Void>() {
@Override
public Void call() throws Exception {
if (currentList != null) {
int index = 0;
for (int i = 0; (i < currentList.size()) && !stopped; i++) {
ScoredChromosomeWindow scw = currentList.get(i);
if (scw.getScore() != 0) {
String name = chromosome.getName() + "." + index++;
int start = scw.getStart();
int stop = scw.getStop();
float score = scw.getScore();
Gene geneToAdd = new SimpleGene(name,
Strand.FIVE,
start,
stop,
score,
SCWListViews.createGenericSCWListView(start, stop, score));
resultListBuilder.addElementToBuild(chromosome, geneToAdd);
}
}
}
// tell the operation pool that a chromosome is done
op.notifyDone();
return null;
}
};
threadList.add(currentThread);
}
op.startPool(threadList);
List<ListView<Gene>> data = resultListBuilder.getGenomicList();
return new SimpleGeneList(data, GeneScoreType.MAXIMUM_COVERAGE, 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;
}
}