/*******************************************************************************
* 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.geneList;
import java.io.IOException;
import java.io.ObjectInputStream;
import java.io.ObjectOutputStream;
import java.util.List;
import java.util.concurrent.ExecutionException;
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.GeneScoreType;
import edu.yu.einstein.genplay.dataStructure.gene.Gene;
import edu.yu.einstein.genplay.dataStructure.list.chromosomeWideList.geneListView.GeneListView;
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;
/**
* Simple implementation of the {@link GeneList} interface.
* @author Julien Lajugie
*/
public final class SimpleGeneList extends AbstractListView<ListView<Gene>> implements GeneList {
/** Generated serial ID */
private static final long serialVersionUID = 2409860942228135092L;
/** Version number of the class */
private static final transient int CLASS_VERSION_NUMBER = 0;
/** {@link GenomicDataArrayList} containing the Genes */
private final ListView<Gene>[] data;
/** URL to a gene database that can be used to search information about the genes of this list */
private final String geneDBURL;
/** Type of the scores of the genes and exons of this list (RPKM, max, sum) */
private final GeneScoreType geneScoreType;
/** Object that searches genes and handle funtion such as find next, find previous */
private transient GeneSearcher geneSearcher;
/**
* Creates an instance of {@link SimpleGeneList}
* @param data list of genes organized by chromosome
* @param geneScoreType type of the scores of the genes and exons (RPKM, max, sum)
* @param geneDBURL URL of the gene database
* @throws ExecutionException
* @throws InterruptedException
*/
public SimpleGeneList(List<ListView<Gene>> data, GeneScoreType geneScoreType, String geneDBURL) throws InterruptedException, ExecutionException {
super();
ProjectChromosomes projectChromosomes = ProjectManager.getInstance().getProjectChromosomes();
this.data = new GeneListView[projectChromosomes.size()];
for (int i = 0; i < projectChromosomes.size(); i++){
if (i < data.size()) {
this.data[i] = data.get(i);
}
}
this.geneDBURL = geneDBURL;
this.geneScoreType = geneScoreType;
geneSearcher = new GeneSearcher(this);
}
@Override
public ListView<Gene> get(Chromosome chromosome) throws InvalidChromosomeException {
ProjectChromosomes projectChromosomes = ProjectManager.getInstance().getProjectChromosomes();
int index = projectChromosomes.getIndex(chromosome);
return get(index);
}
@Override
public Gene get(Chromosome chromosome, int index) throws InvalidChromosomeException {
return get(chromosome).get(index);
}
@Override
public ListView<Gene> get(int chromosomeIndex) {
return data[chromosomeIndex];
}
@Override
public Gene get(int chromosomeIndex, int elementIndex) {
return get(chromosomeIndex).get(elementIndex);
}
@Override
public String getGeneDBURL() {
return geneDBURL;
}
@Override
public GeneScoreType getGeneScoreType() {
return geneScoreType;
}
@Override
public GeneSearcher getGeneSearcher() {
return geneSearcher;
}
/**
* Method used for deserialization
* @param in
* @throws IOException
* @throws ClassNotFoundException
*/
private void readObject(ObjectInputStream in) throws IOException, ClassNotFoundException {
in.readInt();
// read final fields
in.defaultReadObject();
// set the gene searcher
geneSearcher = new GeneSearcher(this);
}
@Override
public int size() {
return data.length;
}
@Override
public int size(Chromosome chromosome) throws InvalidChromosomeException {
return get(chromosome).size();
}
@Override
public int size(int index) {
return get(index).size();
}
/**
* Method used for serialization
* @param out
* @throws IOException
*/
private void writeObject(ObjectOutputStream out) throws IOException {
out.writeInt(CLASS_VERSION_NUMBER);
out.defaultWriteObject();
}
}