/*
* Eoulsan development code
*
* This code may be freely distributed and modified under the
* terms of the GNU Lesser General Public License version 2.1 or
* later and CeCILL-C. This should be distributed with the code.
* If you do not have a copy, see:
*
* http://www.gnu.org/licenses/lgpl-2.1.txt
* http://www.cecill.info/licences/Licence_CeCILL-C_V1-en.txt
*
* Copyright for this code is held jointly by the Genomic platform
* of the Institut de Biologie de l'École normale supérieure and
* the individual authors. These should be listed in @author doc
* comments.
*
* For more information on the Eoulsan project and its aims,
* or to join the Eoulsan Google group, visit the home page
* at:
*
* http://outils.genomique.biologie.ens.fr/eoulsan
*
*/
package fr.ens.biologie.genomique.eoulsan.data.storages;
import java.util.Map;
import fr.ens.biologie.genomique.eoulsan.bio.GenomeDescription;
import fr.ens.biologie.genomique.eoulsan.bio.readsmappers.SequenceReadsMapper;
import fr.ens.biologie.genomique.eoulsan.data.DataFile;
/**
* This interface define a genome index storage.
* @since 1.1
* @author Laurent Jourdren
*/
public interface GenomeIndexStorage {
/**
* Get the DataFile that corresponds to a mapper and a genome
* @param mapper mapper
* @param genome genome description object for the genome
* @param additionalDescription description of the additional parameters
* @return a DataFile that contains the path to the index or null if the index
* has not yet been computed
*/
DataFile get(SequenceReadsMapper mapper, GenomeDescription genome,
Map<String, String> additionalDescription);
/**
* Put the index archive in the storage.
* @param mapper mapper
* @param genome genome description object
* @param additionalDescription description of the additional parameters
* @param indexArchive the DataFile that contains the index
*/
void put(SequenceReadsMapper mapper, GenomeDescription genome,
Map<String, String> additionalDescription, DataFile indexArchive);
}