GLOGeneRenamer.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.io.BufferedReader;
import java.io.File;
import java.io.FileReader;
import java.util.HashMap;
import java.util.Map;

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.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.ListViewBuilder;
import edu.yu.einstein.genplay.util.Utils;


/**
 * Renames the genes of a list with new names specified in a file with the following format:
 * oldName \t newName
 * @author Julien Lajugie
 */
public class GLOGeneRenamer implements Operation<GeneList> {

	private final GeneList 	geneList;			// input geneList
	private final File 		file;				// file in which the gene needs to be renamed
	private boolean			stopped = false;	// true if the operation must be stopped


	/**
	 * Creates an instance of {@link GLOGeneRenamer}
	 * @param geneList list of genes
	 * @param fileName file name contain
	 */
	public GLOGeneRenamer(GeneList geneList, File fileName) {
		this.geneList = geneList;
		file = fileName;
	}


	@Override
	public GeneList compute() throws Exception {
		BufferedReader bufReader = null;
		try {
			bufReader = new BufferedReader(new FileReader(file));
			Map<String, String> nameMap = new HashMap<String, String>();
			String lineRead;
			while (((lineRead = bufReader.readLine()) != null) && !stopped) {
				String[] splitLine =  Utils.splitWithTab(lineRead);
				if (splitLine.length > 1) {
					if (!nameMap.containsKey(splitLine[1])) {
						nameMap.put(splitLine[1], splitLine[0]);
					}
				}
			}

			ListViewBuilder<Gene> lvbPrototype = new GeneListViewBuilder();
			final ListOfListViewBuilder<Gene> resultListBuilder = new ListOfListViewBuilder<Gene>(lvbPrototype);
			ProjectChromosomes projectChromosomes = ProjectManager.getInstance().getProjectChromosomes();
			for (final Chromosome chromosome: projectChromosomes) {
				for (int j = 0; (j < geneList.size(chromosome)) && !stopped; j++) {
					Gene currentGene = geneList.get(chromosome,  j);
					String newName = null;
					Gene geneToAdd;
					if ((newName = nameMap.get(currentGene.getName())) != null) {
						geneToAdd = new SimpleGene(
								newName,
								currentGene.getStrand(),
								currentGene.getStart(),
								currentGene.getStop(),
								currentGene.getScore(),
								currentGene.getUTR5Bound(),
								currentGene.getUTR3Bound(),
								currentGene.getExons()
								);
					} else {
						geneToAdd = currentGene;
					}
					resultListBuilder.addElementToBuild(chromosome, geneToAdd);
				}
			}
			return new SimpleGeneList(resultListBuilder.getGenomicList(), geneList.getGeneScoreType(), geneList.getGeneDBURL());
		} finally {
			if (bufReader != null) {
				bufReader.close();
			}
		}
	}


	@Override
	public String getDescription() {
		return "Operation: Rename Genes, input file: " + file.getName();
	}


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


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


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