/*******************************************************************************
* 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.utils;
import java.util.List;
/**
* @author Nicolas Fourel
* @version 0.1
*/
public interface VCFGenomeIndexer {
/**
* @param genomeRawName a raw name of a genome
* @return the index of the column within a VCF file for the one the given genome name is related to.
*/
public int getIndexFromRawGenomeName (String genomeRawName);
/**
* @param genomeFullName a raw name of a genome
* @return the index of the column within a VCF file for the one the given genome name is related to.
*/
public int getIndexFromFullGenomeName (String genomeFullName);
/**
* @param index index of a column in a VCF file
* @return the raw name of the genome related to the index of a column
*/
public String getGenomeRawName (int index);
/**
* @return the list of genome raw names
*/
public List<String> getGenomeRawNames ();
}