/*******************************************************************************
* 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.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.ScoreOperation;
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;
/**
* Defines regions as "islands" of non zero value bins
* separated by more than a specified number of zero value bins.
* Computes the average on these regions.
* Returns a new {@link GeneList} with the defined regions having their average/max/sum as a score
* @author Chirag Gorasia
*/
public class SCWLOTransfragGeneList implements Operation<GeneList> {
private final SCWList scwList; // input list
private final int zeroSCWGap; // minimum size of the gap separating two intervals
private final ScoreOperation operation; // operation to use to compute the score of the intervals
private boolean stopped = false; // true if the operation must be stopped
/**
* Creates an instance of {@link SCWLOTransfrag}
* @param scwList input list
* @param zeroSCWGap minimum size of the gap separating two intervals
* @param operation operation to use to compute the score of the intervals
*/
public SCWLOTransfragGeneList(SCWList scwList, int zeroSCWGap, ScoreOperation operation) {
this.scwList = scwList;
this.zeroSCWGap = zeroSCWGap;
this.operation = operation;
}
@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> builderPrototype = new GeneListViewBuilder();
final ListOfListViewBuilder<Gene> resultListBuilder = new ListOfListViewBuilder<Gene>(builderPrototype);
for (final Chromosome chromosome: projectChromosomes) {
final ListView<ScoredChromosomeWindow> currentList = scwList.get(chromosome);
Callable<Void> currentThread = new Callable<Void>() {
@Override
public Void call() throws Exception {
Gene newGene;
if ((currentList != null) && (currentList.size() != 0)) {
int geneCounter = 1;
int j = 0;
while ((j < currentList.size()) && !stopped) {
// skip zero values
while ((j < currentList.size()) && (currentList.get(j).getScore() == 0) &&!stopped) {
j++;
}
int regionStartIndex = j;
int regionStopIndex = regionStartIndex;
ListView<ScoredChromosomeWindow> exons;
int gapSize = 0;
// a region stops when there is maxZeroWindowGap consecutive zero bins
while (((j + 1) < currentList.size()) && (gapSize <= zeroSCWGap) && !stopped) {
regionStopIndex = j;
if (currentList.get(j + 1).getScore() == 0) {
gapSize += currentList.get(j + 1).getSize();
} else if (currentList.get(j + 1).getStart() != currentList.get(j).getStop()) {
gapSize += currentList.get(j + 1).getStart() - currentList.get(j).getStop();
} else {
gapSize = 0;
}
j++;
}
j = regionStopIndex;
if (regionStopIndex >= currentList.size()) {
regionStopIndex = currentList.size()-1;
}
if (regionStopIndex >= regionStartIndex) {
float regionScore = 0;
if (operation == ScoreOperation.AVERAGE) {
// all the windows of the region are set with the average value on the region
regionScore = (float) SCWListViews.average(currentList, regionStartIndex, regionStopIndex);
} else if (operation == ScoreOperation.MAXIMUM) {
// all the windows of the region are set with the max value on the region
regionScore = SCWListViews.maxNoZero(currentList, regionStartIndex, regionStopIndex);
} else {
// all the windows of the region are set with the sum value on the region
regionScore = (float) SCWListViews.sum(currentList, regionStartIndex, regionStopIndex);
}
int regionStart = currentList.get(regionStartIndex).getStart();
int regionStop = currentList.get(regionStopIndex).getStop();
exons = SCWListViews.createGenericSCWListView(regionStart, regionStop, regionScore);
newGene = new SimpleGene(chromosome.getName() + "." + Integer.toString(geneCounter++), Strand.get('+'), regionStart, regionStop, regionScore, exons);
resultListBuilder.addElementToBuild(chromosome, newGene);
}
j++;
}
}
// tell the operation pool that a chromosome is done
op.notifyDone();
return null;
}
};
threadList.add(currentThread);
}
op.startPool(threadList);
return new SimpleGeneList(resultListBuilder.getGenomicList(), null, null);
}
@Override
public String getDescription() {
return "Operation: Transfrag, Gap Size = " + zeroSCWGap + " Zero Value Successive Bins";
}
@Override
public String getProcessingDescription() {
return "Computing Transfrag";
}
@Override
public int getStepCount() {
return 1;
}
@Override
public void stop() {
stopped = true;
}
}