ChromosomeWindowListViews.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.util.ListView;

import edu.yu.einstein.genplay.core.comparator.ChromosomeWindowStartComparator;
import edu.yu.einstein.genplay.dataStructure.chromosomeWindow.ChromosomeWindow;
import edu.yu.einstein.genplay.dataStructure.chromosomeWindow.SimpleChromosomeWindow;
import edu.yu.einstein.genplay.dataStructure.genomeWindow.GenomeWindow;
import edu.yu.einstein.genplay.dataStructure.list.genomeWideList.GenomicListView;
import edu.yu.einstein.genplay.dataStructure.list.listView.ListView;


/**
 * Provides utilities for {@link ListView} objects of items implementing {@link ChromosomeWindow}.
 * @author Julien Lajugie
 */
public class ChromosomeWindowListViews {

	/**
	 * @param list a {@link GenomicListView} of objects that extends {@link ChromosomeWindow}
	 * @param genomeWindow a {@link GenomeWindow}
	 * @return the chromosome windows of the input list that are located in the specified genome window (including elements that are not fully in the window)
	 */
	public static final <T extends ChromosomeWindow> ListView<T> subList(GenomicListView<T> list, GenomeWindow genomeWindow) {
		return subList(list.get(genomeWindow.getChromosome()), genomeWindow.getStart(), genomeWindow.getStop());
	}


	/**
	 * @param list a {@link ListView} of objects that extends {@link ChromosomeWindow}
	 * @param start a start position
	 * @param stop a stop position
	 * @return a {@link ListView} that contains all the elements of the input list that are located between the start and stop positions.
	 * The elements that are not fully between the specified positions are still included.
	 */
	public static final <T extends ChromosomeWindow> ListView<T> subList(ListView<T> list, int start, int stop) {
		ChromosomeWindow startChromosomeWindow = new SimpleChromosomeWindow(start, start);
		ChromosomeWindow stopChromosomeWindow = new SimpleChromosomeWindow(stop, stop);

		// search the start
		int indexStart = ListViews.binarySearch(list, startChromosomeWindow, new ChromosomeWindowStartComparator());
		if (indexStart < 0) {
			indexStart = -indexStart - 1;
		}
		// and the previous element if its stop is after the specified start position
		if ((indexStart > 0) && (list.get(indexStart - 1).getStop() > start)) {
			indexStart--;
		}

		// search the stop
		int indexStop = ListViews.binarySearch(list, stopChromosomeWindow, new ChromosomeWindowStartComparator());
		if (indexStop < 0) {
			indexStop = -indexStop - 1;
		}
		indexStop = Math.min(list.size(), indexStop);
		return list.subList(indexStart, indexStop);
	}
}