/******************************************************************************* * 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.security.InvalidParameterException; import java.util.ArrayList; import java.util.Collection; 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.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.util.NumberFormats; /** * Applies a gaussian filter on the BinList and returns the result in a new BinList. * @author Julien Lajugie */ public class BLOGauss implements Operation<BinList> { private final BinList binList; // input list private final int movingWindowWidth; // size of the moving window in bp private final boolean fillNullValues; // true to fill the null values private boolean stopped = false; // true if the operation must be stopped /** * Creates an instance of {@link BLOGauss} * Applies a gaussian filter on the BinList and returns the result in a new BinList. * @param binList {@link BinList} to gauss * @param movingWindowWidth size of the moving window in bp * @param fillNullValues set to true to fill the null values */ public BLOGauss(BinList binList, int movingWindowWidth, boolean fillNullValues) { this.binList = binList; this.movingWindowWidth = movingWindowWidth; this.fillNullValues = fillNullValues; } @Override public BinList compute() throws InvalidParameterException, InterruptedException, ExecutionException, CloneNotSupportedException { final int binSize = binList.getBinSize(); final int sigma = movingWindowWidth / 4; final int halfWidth = movingWindowWidth / 2 / binSize; // we create an array of coefficients. The index correspond to a distance and for each distance we calculate a coefficient final double[] coefTab = new double[halfWidth + 1]; // compute the gaussian coefficients double gaussianCoefConst1 = 1 / (Math.sqrt(2.0 * Math.PI * sigma)); double gaussianCoefConst2 = 2.0 * Math.pow(sigma, 2); for(int i = 0; i <= halfWidth; i++) { coefTab[i] = gaussianCoefConst1 * Math.exp(-(Math.pow((i * binSize), 2) / gaussianCoefConst2)); } ProjectChromosomes projectChromosomes = ProjectManager.getInstance().getProjectChromosomes(); final OperationPool op = OperationPool.getInstance(); final Collection<Callable<Void>> threadList = new ArrayList<Callable<Void>>(); final BinListBuilder resultListBuilder = new BinListBuilder(binList.getBinSize()); for (final Chromosome chromosome: projectChromosomes) { final ListView<ScoredChromosomeWindow> currentList = binList.get(chromosome); Callable<Void> currentThread = new Callable<Void>() { @Override public Void call() throws Exception { if (currentList != null) { for(int j = 0; (j < currentList.size()) && !stopped; j++) { float score = 0f; if ((currentList.get(j).getScore() != 0) || (fillNullValues)) { // apply the array of coefficients centered on the current value to gauss double SumCoef = 0; double SumNormSignalCoef = 0; for (int k = -halfWidth; (k <= halfWidth) && !stopped; k++) { if(((j + k) >= 0) && ((j + k) < currentList.size())) { int distance = Math.abs(k); if(currentList.get(j + k).getScore() != 0) { SumCoef += coefTab[distance]; SumNormSignalCoef += coefTab[distance] * currentList.get(j + k).getScore(); } } } if(SumCoef != 0) { score = (float) (SumNormSignalCoef / SumCoef); } } resultListBuilder.addElementToBuild(chromosome, score); } } op.notifyDone(); return null; } }; threadList.add(currentThread); } op.startPool(threadList); return (BinList) resultListBuilder.getSCWList(); } @Override public String getDescription() { final int sigma = movingWindowWidth / 4; return "Operation: Gauss, Sigma = " + NumberFormats.getPositionFormat().format(sigma) + "bp, Moving Window = " + NumberFormats.getPositionFormat().format(movingWindowWidth) +"bp"; } @Override public String getProcessingDescription() { return "Gaussing"; } @Override public int getStepCount() { return binList.getCreationStepCount() + 1; } @Override public void stop() { stopped = true; } }