/*******************************************************************************
* 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.repeatFamilyList;
import java.io.IOException;
import java.util.concurrent.ExecutionException;
import edu.yu.einstein.genplay.core.IO.dataReader.RepeatReader;
import edu.yu.einstein.genplay.dataStructure.chromosomeWindow.ChromosomeWindow;
import edu.yu.einstein.genplay.dataStructure.chromosomeWindow.SimpleChromosomeWindow;
import edu.yu.einstein.genplay.exception.exceptions.InvalidChromosomeException;
import edu.yu.einstein.genplay.exception.exceptions.ObjectAlreadyBuiltException;
/**
* Factory class for vending {@link SimpleRepeatFamilyList} objects.
* @author Julien Lajugie
*/
public class SimpleRepeatFamilyListFactory {
/**
* Creates a {@link RepeatFamilyList} from the data retrieved by the specified {@link RepeatReader}.
* @param repeatReader a {@link RepeatReader}
* @return a {@link RepeatFamilyList}
* @throws ExecutionException
* @throws InterruptedException
* @throws CloneNotSupportedException
* @throws IOException
* @throws ObjectAlreadyBuiltException
* @throws InvalidChromosomeException
*/
public static RepeatFamilyList createRepeatList(RepeatReader repeatReader) throws InterruptedException, ExecutionException, CloneNotSupportedException, InvalidChromosomeException, ObjectAlreadyBuiltException, IOException {
RepeatFamilyListBuilder builder = new RepeatFamilyListBuilder();
while (repeatReader.readItem()) {
ChromosomeWindow currentWindow = new SimpleChromosomeWindow(repeatReader.getStart(), repeatReader.getStop());
builder.addElementToBuild(repeatReader.getChromosome(), repeatReader.getName(), currentWindow);
}
return new SimpleRepeatFamilyList(builder.getGenomicList());
}
}