/*******************************************************************************
* 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.IO.utils;
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.exception.exceptions.InvalidChromosomeException;
/**
* Used by extractors to define the chromosomes that need to be extracted.
* @author Julien Lajugie
*/
public class ChromosomesSelector {
/** Map of chromosome names associated with a boolean set to true if the chromosome should be extracted and false if not.
* If the map is null, all chromosomes need to be extracted
*/
private final Map<String, Boolean> chromosomeSelection;
/** Index of the last selected chromosome */
private final int indexLastChromosome;
/** Save a reference to the {@link ProjectChromosomes} for fast retrieval */
private final ProjectChromosomes projectChromosomes;
/**
* Creates an instance of {@link ChromosomesSelector}
* @param chromosomeSelection chromosome to extract
*/
public ChromosomesSelector(boolean[] chromosomeSelection) {
projectChromosomes = ProjectManager.getInstance().getProjectChromosomes();
this.chromosomeSelection = new HashMap<String, Boolean>();
int indexLastChromosomeTmp = Integer.MAX_VALUE;
for (int i = 0; i < projectChromosomes.size(); i++) {
if (chromosomeSelection[i]) {
indexLastChromosomeTmp = i;
}
this.chromosomeSelection.put(projectChromosomes.get(i).getName(), chromosomeSelection[i]);
}
indexLastChromosome = indexLastChromosomeTmp;
}
/**
* @param chromosomeName name of a chromosome
* @return true if the specified chromosome is after the last selected has already been extracted.
* The order of chromosomes is defined by the {@link ProjectChromosomes}
*/
public final boolean isExtractionDone(String chromosomeName) {
try {
return projectChromosomes.getIndex(chromosomeName) > indexLastChromosome;
} catch (InvalidChromosomeException e) {
return false;
}
}
/**
* @param chromosomeName name of a chromosome
* @return true if the specified chromosome was set to be extracted. False otherwise.
*/
public final boolean isSelected(String chromosomeName) {
if (chromosomeSelection == null) {
return true;
}
Boolean isSelected = chromosomeSelection.get(chromosomeName);
return (isSelected != null) && isSelected;
}
}