/*******************************************************************************
* 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;
import java.io.Serializable;
import edu.yu.einstein.genplay.dataStructure.chromosome.Chromosome;
import edu.yu.einstein.genplay.dataStructure.list.listView.ListView;
import edu.yu.einstein.genplay.exception.exceptions.InvalidChromosomeException;
/**
* This class represents an immutable list of object organized by chromosome
* @param <T> type of the objects stored in the list
* @author Julien Lajugie
*/
public interface GenomicListView<T> extends Serializable, Iterable<ListView<T>>, ListView<ListView<T>> {
/**
* @param chromosome a {@link Chromosome}
* @return the {@link ListView} associated to the specified {@link Chromosome}. The returned list is immutable (read only)
* @throws InvalidChromosomeException
*/
public ListView<T> get(Chromosome chromosome) throws InvalidChromosomeException;
/**
* @param chromosome index of a chromosome
* @param index
* @return the data with the specified index on the specified chromosome
* @throws InvalidChromosomeException
*/
public T get(Chromosome chromosome, int index) throws InvalidChromosomeException;
/**
* @param chromosomeIndex index of a chromosome
* @param elementIndex
* @return the data with the specified index on the specified chromosome
*/
public T get(int chromosomeIndex, int elementIndex);
/**
* @return true if the {@link ListView} contains no elements
*/
@Override
public boolean isEmpty();
/**
* @return the number of chromosome lists.
*/
@Override
public int size();
/**
* @param chromosome
* @return the size of the list for a specified chromosome
* @throws InvalidChromosomeException
*/
public int size(Chromosome chromosome) throws InvalidChromosomeException;
/**
* @param chromosomeIndex index of a chromosome
* @return the size of the list for the specified chromosome
*/
public int size(int chromosomeIndex);
}