Package fr.ens.biologie.genomique.aozan

Class Storages

java.lang.Object

fr.ens.biologie.genomique.aozan.Storages

public class Storages
extends Object

This class define storage for FastQ Screen.

Since:

3.0

Author:

Laurent Jourdren

Method Summary

Modifier and Type	Method	Description
fr.ens.biologie.genomique.kenetre.bio.GenomeDescription	createGenomeDescription(File genomePath)	Create a GenomeDescription object from a Fasta file.
fr.ens.biologie.genomique.kenetre.storage.GenomeDescStorage	getGenomeDescStorage()	Get the genome description storage.
fr.ens.biologie.genomique.kenetre.storage.GenomeIndexStorage	getGenomeIndexStorage()	Get the genome index storage.
fr.ens.biologie.genomique.kenetre.storage.FileStorage	getGenomeStorage()	Get the genome storage.
static Storages	getInstance()	Get the instance of the singleton.
static void	init(String genomeStoragePath, String genomeDescStoragePath, String genomeMapperIndexStoragePath, fr.ens.biologie.genomique.kenetre.log.GenericLogger logger)	Initialize the singleton.
boolean	isGenomeDescStorage()	Test if a genome description storage exists.
boolean	isGenomeIndexStorage()	Test if a genome index storage exists.
boolean	isGenomeStorage()	Test if a genome storage exists.
static boolean	isInstance()	Test if the instance of the singleton has been initialized.

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Method Detail

isGenomeDescStorage

public boolean isGenomeDescStorage()

Test if a genome description storage exists.

Returns:

true if a genome description storage exists

isGenomeIndexStorage

public boolean isGenomeIndexStorage()

Test if a genome index storage exists.

Returns:

true if a genome index storage exists

isGenomeStorage

public boolean isGenomeStorage()

Test if a genome storage exists.

Returns:

true if a genome storage exists

getGenomeDescStorage

public fr.ens.biologie.genomique.kenetre.storage.GenomeDescStorage getGenomeDescStorage()

Get the genome description storage.

Returns:

the genome description storage object

getGenomeIndexStorage

public fr.ens.biologie.genomique.kenetre.storage.GenomeIndexStorage getGenomeIndexStorage()

Get the genome index storage.

Returns:

the genome index storage object

getGenomeStorage

public fr.ens.biologie.genomique.kenetre.storage.FileStorage getGenomeStorage()

Get the genome storage.

Returns:

the genome index object

createGenomeDescription

public fr.ens.biologie.genomique.kenetre.bio.GenomeDescription createGenomeDescription(File genomePath)
                                                                                throws fr.ens.biologie.genomique.kenetre.bio.BadBioEntryException,
                                                                                       IOException

Create a GenomeDescription object from a Fasta file.

Parameters:

genomePath - genome path

Throws:

fr.ens.biologie.genomique.kenetre.bio.BadBioEntryException - if an error occurs during create genome description object

IOException - if an error occurs during access genome file

isInstance

public static boolean isInstance()

Test if the instance of the singleton has been initialized.

Returns:

true if the instance of the singleton has been initialized

init

public static void init(String genomeStoragePath,
                        String genomeDescStoragePath,
                        String genomeMapperIndexStoragePath,
                        fr.ens.biologie.genomique.kenetre.log.GenericLogger logger)

Initialize the singleton.

Parameters:

genomeStoragePath - path of the genomes storage

genomeDescStoragePath - path of the genome descriptions storage

genomeMapperIndexStoragePath - the genome indexes storage

logger - the logger for the storage

getInstance

public static Storages getInstance()

Get the instance of the singleton.

Returns:

the instance of the singleton or an exception if the instance has not been initialized