SCWListWriter.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.SCWListWriter;

import java.io.File;

import edu.yu.einstein.genplay.core.IO.writer.Writer;
import edu.yu.einstein.genplay.core.manager.project.ProjectChromosomes;
import edu.yu.einstein.genplay.core.manager.project.ProjectManager;
import edu.yu.einstein.genplay.dataStructure.enums.AlleleType;
import edu.yu.einstein.genplay.dataStructure.list.genomeWideList.SCWList.SCWList;



/**
 * Abstract class that must be extended by the classes able to write a {@link SCWList} into a file
 * @author Julien Lajugie
 * @version 0.1
 */
public abstract class SCWListWriter implements Writer {

	protected final ProjectChromosomes			projectChromosomes;	// ChromosomeManager
	protected final File 						outputFile;			// output file
	protected final SCWList	data;				// data to print
	protected final String						name;				// name of the BinList

	protected String							fullGenomeName;		// the genome name (multi genome project only)
	protected AlleleType						allele;				// the allele type (multi genome project only)


	/**
	 * Constructor
	 * @param outputFile output {@link File}
	 * @param data {@link SCWList} to write
	 * @param name a name for the data
	 */
	public SCWListWriter(File outputFile, SCWList data, String name) {
		this.projectChromosomes = ProjectManager.getInstance().getProjectChromosomes();
		this.outputFile = outputFile;
		this.data = data;
		this.name = name;
	}


	@Override
	public void setMultiGenomeCoordinateSystem (String genome, AlleleType allele) {
		this.fullGenomeName = genome;
		this.allele = allele;
	}
}