GLOFilterThreshold.java

/*******************************************************************************
 * 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.geneList;

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.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.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;


/**
 * Removes the genes with an overall RPKM above and under specified thresholds
 * @author Julien Lajugie
 */
public class GLOFilterThreshold implements Operation<GeneList> {
	private final GeneList 			geneList;			// input list
	private final float 			lowThreshold;		// filters the genes with an overall RPKM under this threshold
	private final float 			highThreshold;		// filters the genes with an overall RPKM above this threshold
	private final boolean			isSaturation;		// true if we saturate, false if we remove the filtered values
	private boolean					stopped = false;	// true if the operation must be stopped


	/**
	 * Creates an instance of {@link GLOFilterThreshold}
	 * @param geneList input list
	 * @param lowThreshold filters the genes with an overall RPKM under this threshold
	 * @param highThreshold filters the genes with an overall RPKM above this threshold
	 * @param isSaturation true to saturate, false to remove the filtered values
	 */
	public GLOFilterThreshold(GeneList geneList, float	lowThreshold, float highThreshold, boolean isSaturation) {
		this.geneList = geneList;
		this.lowThreshold = lowThreshold;
		this.highThreshold = highThreshold;
		this.isSaturation = isSaturation;
	}


	@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<Gene> currentList = geneList.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++) {
							Gene currentGene = currentList.get(j);

							if ((!Float.isNaN(currentGene.getScore()))) {
								Gene geneToAdd = null;
								if (currentGene.getScore() > highThreshold) {
									// if the score is greater than the high threshold
									if (isSaturation) {
										// set the value to high threshold (saturation)
										geneToAdd = new SimpleGene(
												currentGene.getName(),
												currentGene.getStrand(),
												currentGene.getStart(),
												currentGene.getStop(),
												highThreshold,
												currentGene.getUTR5Bound(),
												currentGene.getUTR3Bound(),
												currentGene.getExons()
												);
									}
								} else if (currentGene.getScore() < lowThreshold) {
									// if the score is smaller than the low threshold
									if (isSaturation) {
										// set the value to low threshold (saturation)
										geneToAdd = new SimpleGene(
												currentGene.getName(),
												currentGene.getStrand(),
												currentGene.getStart(),
												currentGene.getStop(),
												lowThreshold,
												currentGene.getUTR5Bound(),
												currentGene.getUTR3Bound(),
												currentGene.getExons()
												);
									}
								} else {
									// if the score is between the two threshold
									geneToAdd = currentGene;
								}
								if (geneToAdd != null) {
									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, geneList.getGeneScoreType(), geneList.getGeneDBURL());
	}


	@Override
	public String getDescription() {
		String optionStr;
		if (isSaturation) {
			optionStr = ", option = saturation";
		} else {
			optionStr = ", option = remove";
		}
		return "Operation: Threshold Filter, minimum = " + lowThreshold + ", maximum = " + highThreshold + optionStr;
	}


	@Override
	public String getProcessingDescription() {
		return "Filtering Genes";
	}


	@Override
	public int getStepCount() {
		return 1;
	}


	@Override
	public void stop() {
		stopped = true;
	}
}