/******************************************************************************* * 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; } } }