BinListAsWiggleWriter.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.IO.writer.binListWriter;

import java.io.BufferedWriter;
import java.io.File;
import java.io.FileWriter;
import java.io.IOException;

import edu.yu.einstein.genplay.core.manager.project.ProjectManager;
import edu.yu.einstein.genplay.core.multiGenome.utils.FormattedMultiGenomeName;
import edu.yu.einstein.genplay.core.multiGenome.utils.ShiftCompute;
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.listView.ListView;
import edu.yu.einstein.genplay.dataStructure.scoredChromosomeWindow.ScoredChromosomeWindow;
import edu.yu.einstein.genplay.gui.statusBar.Stoppable;
import edu.yu.einstein.genplay.util.NumberFormats;


/**
 * Writes {@link BinList} data into Wiggle files.
 * @author Julien Lajugie
 */
public final class BinListAsWiggleWriter extends BinListWriter implements Stoppable {

	private static final int ZERO_COUNT = 15;	// how many successive 0 values are needed to print a new a header line
	private boolean needsToBeStopped = false;	// true if the writer needs to be stopped


	/**
	 * Creates an instance of {@link BinListAsWiggleWriter}.
	 * @param outputFile output {@link File}
	 * @param data {@link BinList} to write
	 * @param name a name for the {@link BinList}
	 */
	public BinListAsWiggleWriter(File outputFile, BinList data, String name) {
		super(outputFile, data, name);
	}


	/**
	 * Stops the writer while it's writing a file
	 */
	@Override
	public void stop() {
		needsToBeStopped = true;
	}


	@Override
	public void write() throws IOException, InterruptedException {
		BufferedWriter writer = null;
		try {
			boolean isMultiGenome = ProjectManager.getInstance().isMultiGenomeProject() && (fullGenomeName != null) && (allele != null);

			// try to create a output file
			writer = new BufferedWriter(new FileWriter(outputFile));
			// print the title of the graph
			writer.write("track type=wiggle name=" + name);
			writer.newLine();
			int binSize = data.getBinSize();
			// print the data
			for(Chromosome currentChromosome: projectChromosomes) {
				if(data.get(currentChromosome) != null) {
					ListView<ScoredChromosomeWindow> currentList = data.get(currentChromosome);
					int j = 0;
					// loop until we find a value different from 0
					while ((j < currentList.size()) && (currentList.get(j).getScore() == 0)) {
						j++;
					}
					while (j < currentList.size()) {
						int start = currentList.get(j).getStart();
						if (isMultiGenome) {
							start = ShiftCompute.getPosition(FormattedMultiGenomeName.META_GENOME_NAME, allele, start, currentChromosome, fullGenomeName);
						}

						if (start > -1) {
							// we print a header
							writer.write("fixedStep chrom=" + currentChromosome.getName() + " start=" + start + " step=" + binSize + " span=" + binSize);
							writer.newLine();
							int cpt = 0;
							// if there is more than ZERO_COUNT 0 values we print a new header
							while ((j < currentList.size()) && ((cpt < ZERO_COUNT) || (currentList.get(j).getScore() == 0))) {
								// if the operation need to be stopped we close the writer and delete the file
								if (needsToBeStopped) {
									writer.close();
									outputFile.delete();
									throw new InterruptedException();
								}
								if (currentList.get(j).getScore() == 0) {
									cpt++;
								} else {
									if (cpt != 0) {
										// case where there were less than ZERO_COUNT 0 values so we need to print them
										for (int k = 0; k < cpt; k++) {
											writer.write("0");
											writer.newLine();
										}
										cpt = 0;
									}
									writer.write(NumberFormats.getWriterScoreFormat().format(currentList.get(j).getScore()));
									writer.newLine();
								}
								j++;
							}
						} else {
							j++;
						}
					}
				}
			}
		} finally {
			if (writer != null) {
				writer.close();
			}
		}
	}
}