/*******************************************************************************
* 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.multiGenome.VCF.VCFScanner;
import java.io.IOException;
import edu.yu.einstein.genplay.core.multiGenome.VCF.BGZIPReader;
import edu.yu.einstein.genplay.core.multiGenome.VCF.VCFLine;
import edu.yu.einstein.genplay.core.multiGenome.VCF.VCFFile.VCFFile;
import edu.yu.einstein.genplay.exception.ExceptionManager;
/**
* See the {@link VCFScanner} description for further information on scanners.
* The {@link VCFGenomeScanner} will go through all the lines of a {@link VCFFile}.
* All chromosomes will be scanned.
*
* It is technically optimized to avoid memory peaks.
*
* @author Nicolas Fourel
* @version 0.1
*/
public class VCFGenomeScanner extends VCFScanner {
private final BGZIPReader reader; // The gz reader
/**
* Constructor of {@link VCFGenomeScanner}
* @param receiver
* @param vcfFile
* @throws IOException
*/
public VCFGenomeScanner (VCFScannerReceiver receiver, VCFFile vcfFile) throws IOException {
super(receiver, vcfFile);
this.reader = new BGZIPReader(vcfFile);
}
@Override
protected VCFLine getFirstLine() {
return reader.getCurrentLine();
}
@Override
protected VCFLine getNextLine() {
try {
reader.goNextLine();
} catch (IOException e) {
ExceptionManager.getInstance().caughtException(e);
}
return reader.getCurrentLine();
}
@Override
protected void endScan() {
reader.closeStreams();
}
}