/*******************************************************************************
* 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.comparator;
import java.util.Comparator;
import edu.yu.einstein.genplay.core.multiGenome.data.display.variant.ReferenceVariant;
import edu.yu.einstein.genplay.core.multiGenome.data.display.variant.Variant;
/**
* This class is a comparator for variant.
* The comparison is made according to the reference genome position.
*
* @author Nicolas Fourel
* @version 0.1
*/
public class VariantComparator implements Comparator<Variant> {
@Override
public int compare(Variant o1, Variant o2) {
int position1 = o1.getReferenceGenomePosition();
int position2 = o2.getReferenceGenomePosition();
//int position1 = o1.getStart();
//int position2 = o2.getStart();
if (position1 < position2) {
return -1;
} else if (position1 == position2) {
// SNPs are before Indel if start positions are equal because
// Indel actually start 1bp after the position specified in the VCF
boolean isSNP1 = o1.getLength() == 1;
boolean isSNP2 = o2.getLength() == 1;
if (isSNP1 && !isSNP2) {
return -1;
} else if (isSNP2 && !isSNP1) {
return 1;
}
boolean isReference01 = (o1 instanceof ReferenceVariant);
boolean isReference02 = (o2 instanceof ReferenceVariant);
if (isReference01 && !isReference02) {
return 1;
} else if (!isReference01 && isReference02) {
return -1;
}
int length1 = o1.getLength();
int length2 = o2.getLength();
if (length1 > length2) {
return -1; // the longest variant is first
} else if (length1 < length2) {
return 1;
}
return 0;
} else {
return 1;
}
}
}