/*******************************************************************************
* 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.binList;
import java.util.ArrayList;
import java.util.Collection;
import java.util.Collections;
import java.util.List;
import java.util.concurrent.Callable;
import java.util.concurrent.ExecutionException;
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.list.genomeWideList.SCWList.binList.BinList;
import edu.yu.einstein.genplay.dataStructure.list.genomeWideList.SCWList.binList.BinListBuilder;
import edu.yu.einstein.genplay.dataStructure.list.listView.ListView;
import edu.yu.einstein.genplay.dataStructure.scoredChromosomeWindow.ScoredChromosomeWindow;
import edu.yu.einstein.genplay.exception.exceptions.BinListDifferentWindowSizeException;
import edu.yu.einstein.genplay.util.FloatLists;
/**
* Computes the average, the max or the sum of the {@link BinList} on intervals defined by another BinList
* @author Julien Lajugie
*/
public class BLOIntervalsScoring implements Operation<BinList> {
private final BinList intervalList; // BinList defining the intervals
private final BinList valueList; // BinList defining the values for the calculation
private final int percentageAcceptedValues; // the calculation is calculated only on the x% greatest values of each interval
private final ScoreOperation method; // method of calculation
private boolean stopped = false; // true if the operation must be stopped
/**
* Creates an instance of {@link BLOIntervalsScoring}
* Computes the average, the max or the sum of the {@link BinList} on intervals defined by another BinList
* @param intervalList BinList defining the intervals
* @param valueList BinList defining the values for the calculation
* @param percentageAcceptedValues the calculation is calculated only on the x% greatest values of each interval
* @param method method of calculation
*/
public BLOIntervalsScoring(BinList intervalList, BinList valueList, int percentageAcceptedValues, ScoreOperation method) {
this.intervalList = intervalList;
this.valueList = valueList;
this.percentageAcceptedValues = percentageAcceptedValues;
this.method = method;
}
@Override
public BinList compute() throws InterruptedException, ExecutionException, BinListDifferentWindowSizeException, CloneNotSupportedException {
// check if the binList defining the intervals and the binList with the values have the same bin size
if (intervalList.getBinSize() != valueList.getBinSize()) {
throw new BinListDifferentWindowSizeException();
}
ProjectChromosomes projectChromosomes = ProjectManager.getInstance().getProjectChromosomes();
final OperationPool op = OperationPool.getInstance();
final Collection<Callable<Void>> threadList = new ArrayList<Callable<Void>>();
final BinListBuilder resultListBuilder = new BinListBuilder(valueList.getBinSize());
for (final Chromosome chromosome: projectChromosomes) {
final ListView<ScoredChromosomeWindow> currentIntervals = intervalList.get(chromosome);
final ListView<ScoredChromosomeWindow> currentValues = valueList.get(chromosome);
Callable<Void> currentThread = new Callable<Void>() {
@Override
public Void call() throws Exception {
if ((currentIntervals != null) && (currentValues != null)) {
int j = 0;
while ((j < currentIntervals.size()) && (j < currentValues.size()) && !stopped) {
while ((j < currentIntervals.size()) && (j < currentValues.size()) && (currentIntervals.get(j).getScore() == 0) && !stopped) {
resultListBuilder.addElementToBuild(chromosome, currentIntervals.get(j).getScore());
j++;
}
int k = j;
List<Float> values = new ArrayList<Float>();
while ((j < currentIntervals.size()) && (j < currentValues.size()) && (currentIntervals.get(j).getScore() != 0) && !stopped) {
if (currentValues.get(j).getScore() != 0) {
values.add(currentValues.get(j).getScore());
}
j++;
}
if (values.size() > 0) {
Collections.sort(values);
int indexStart = values.size() - (int)((values.size() * (double)percentageAcceptedValues) / 100d);
float result = 0;
switch (method) {
case AVERAGE:
result = FloatLists.average(values, indexStart, values.size() - 1);
break;
case MAXIMUM:
List<Float> listTmp = values.subList(indexStart, values.size() - 1);
if ((listTmp != null) && (listTmp.size() > 0)) {
result = Collections.max(listTmp);
}
break;
case ADDITION:
result = FloatLists.sum(values, indexStart, values.size() - 1);
break;
default:
throw new IllegalArgumentException("Invalid score calculation method");
}
for (; k < j; k++) {
if (k < currentIntervals.size()) {
resultListBuilder.addElementToBuild(chromosome, result);
}
}
}
}
}
// tell the operation pool that a chromosome is done
op.notifyDone();
return null;
}
};
threadList.add(currentThread);
}
op.startPool(threadList);
return (BinList) resultListBuilder.getSCWList();
}
@Override
public String getDescription() {
return "Operation: Calculation on Projection, Accepted Values = " + percentageAcceptedValues + "%, Method = " + method;
}
@Override
public String getProcessingDescription() {
return "Computing Calculation on Projection";
}
@Override
public int getStepCount() {
return intervalList.getCreationStepCount() + 1;
}
@Override
public void stop() {
stopped = true;
}
}