TwoBitSequenceList.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.dataStructure.list.genomeWideList.nucleotideList;

import java.io.File;
import java.io.FileNotFoundException;
import java.io.IOException;
import java.io.ObjectInputStream;
import java.io.ObjectOutputStream;
import java.io.Serializable;
import java.util.ArrayList;
import java.util.List;

import edu.yu.einstein.genplay.core.manager.project.ProjectChromosomes;
import edu.yu.einstein.genplay.core.manager.project.ProjectManager;
import edu.yu.einstein.genplay.dataStructure.chromosome.Chromosome;
import edu.yu.einstein.genplay.dataStructure.enums.AlleleType;
import edu.yu.einstein.genplay.dataStructure.enums.Nucleotide;
import edu.yu.einstein.genplay.dataStructure.list.chromosomeWideList.nucleotideListView.twoBitListView.TwoBitListView;
import edu.yu.einstein.genplay.dataStructure.list.listView.AbstractListView;
import edu.yu.einstein.genplay.dataStructure.list.listView.ListView;
import edu.yu.einstein.genplay.exception.exceptions.InvalidChromosomeException;


/**
 * Reads a 2Bit files and extracts the data from this kind of files.
 * 2bit files are used to store genome sequences in a random access file
 * @author Julien Lajugie
 */
public class TwoBitSequenceList extends AbstractListView<ListView<Nucleotide>> implements Serializable, NucleotideList {

	/** Generated serial ID */
	private static final long serialVersionUID = -2253030492143151302L;

	/** Version number of the class */
	private static final transient int CLASS_VERSION_NUMBER = 0;

	/** Path of the 2bit file  (used for the serialization) */
	private final String filePath;

	/** Genome name for a multi genome project */
	private final String genomeName;

	/** Allele type for a multi genome project */
	private final AlleleType alleleType;

	/** Each element of this list read a chromosome in the file */
	private final List<ListView<Nucleotide>> data;


	/**
	 * Creates an instance of {@link TwoBitSequenceList}
	 * @param filePath path to the 2bit file
	 * @param reverseBytes true if the bytes of multi-byte entities need to be reversed when read
	 * @param genomeName name of the genome the {@link TwoBitSequenceList} represents
	 * @param alleleType 	allele type for a multi genome project
	 * @param data data of the {@link TwoBitSequenceList}
	 * @throws IOException
	 */
	public TwoBitSequenceList(String filePath, boolean reverseBytes, String genomeName, AlleleType alleleType, List<ListView<Nucleotide>> data) throws IOException {
		super();
		this.filePath = filePath;
		this.genomeName = genomeName;
		this.alleleType = alleleType;
		this.data = data;
	}


	/**
	 * Creates a new instance of {@link TwoBitSequenceList} similar to the
	 * one in parameter but reading the specified file instead. This constructor
	 * is handy when the file path has been modified.
	 * @param twoBitSequenceList
	 * @param file
	 * @throws FileNotFoundException
	 */
	public TwoBitSequenceList(TwoBitSequenceList twoBitSequenceList, File file) throws FileNotFoundException {
		// note that we can't just modify the file path of a TwoBitSequenceList objects because they are immutable
		filePath = file.getAbsolutePath();
		genomeName = twoBitSequenceList.genomeName;
		alleleType = twoBitSequenceList.alleleType;
		data = new ArrayList<ListView<Nucleotide>>();
		for (ListView<Nucleotide> currentLV: twoBitSequenceList.data) {
			data.add(new TwoBitListView((TwoBitListView) currentLV, file));
		}
	}


	@Override
	public ListView<Nucleotide> get(Chromosome chromosome) throws InvalidChromosomeException {
		ProjectChromosomes projectChromosomes = ProjectManager.getInstance().getProjectChromosomes();
		int chromosomeIndex = projectChromosomes.getIndex(chromosome);
		return get(chromosomeIndex);
	}


	@Override
	public Nucleotide get(Chromosome chromosome, int index) throws InvalidChromosomeException {
		ProjectChromosomes projectChromosomes = ProjectManager.getInstance().getProjectChromosomes();
		int chromosomeIndex = projectChromosomes.getIndex(chromosome);
		return get(chromosomeIndex, index);
	}


	@Override
	public ListView<Nucleotide> get(int chromosomeIndex) {
		return data.get(chromosomeIndex);
	}


	@Override
	public Nucleotide get(int chromosomeIndex, int elementIndex) {
		return data.get(chromosomeIndex).get(elementIndex);
	}


	/**
	 * @return the allele type for a multi genome project
	 */
	public AlleleType getAlleleType() {
		return alleleType;
	}


	/**
	 * @return the path to the random access file containing the sequences
	 */
	public String getDataFilePath() {
		return filePath;
	}


	/**
	 * @return The genome name for a multi genome project
	 */
	public String getGenomeName() {
		return genomeName;
	}


	@Override
	public String getSequenceFile() {
		return filePath;
	}


	/**
	 * Method used for deserialization
	 * @param in
	 * @throws IOException
	 * @throws ClassNotFoundException
	 */
	private void readObject(ObjectInputStream in) throws IOException, ClassNotFoundException {
		// read the class version number
		in.readInt();
		// read the final fields
		in.defaultReadObject();
	}


	/**
	 * Reinitializes the reader for each {@link ListView}
	 * @throws FileNotFoundException
	 */
	public void reinitDataFile() throws FileNotFoundException {
		for (ListView<Nucleotide> currentList: data) {
			((TwoBitListView) currentList).reinitDataFile();
		}
	}


	@Override
	public int size() {
		return data.size();
	}


	@Override
	public int size(Chromosome chromosome) throws InvalidChromosomeException {
		ProjectChromosomes projectChromosomes = ProjectManager.getInstance().getProjectChromosomes();
		int chromosomeIndex = projectChromosomes.getIndex(chromosome);
		return size(chromosomeIndex);
	}


	@Override
	public int size(int chromosomeIndex) {
		return data.get(chromosomeIndex).size();
	}


	/**
	 * Method used for serialization
	 * @param out
	 * @throws IOException
	 */
	private void writeObject(ObjectOutputStream out) throws IOException {
		// write the class version number
		out.writeInt(CLASS_VERSION_NUMBER);
		// write the final fields
		out.defaultWriteObject();
	}
}