/******************************************************************************* * 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()); } }