Package fr.ens.biologie.genomique.eoulsan.data.storages

Class DataFileGenomeDescStorage

java.lang.Object

fr.ens.biologie.genomique.kenetre.storage.AbstractFileGenomeDescStorage

fr.ens.biologie.genomique.eoulsan.data.storages.DataFileGenomeDescStorage

All Implemented Interfaces:

fr.ens.biologie.genomique.kenetre.storage.GenomeDescStorage

public class DataFileGenomeDescStorage
extends fr.ens.biologie.genomique.kenetre.storage.AbstractFileGenomeDescStorage

This class define a storage for genome description files using DataFile API.

Since:

2.6

Author:

Laurent Jourdren

Field Summary

Fields inherited from class fr.ens.biologie.genomique.kenetre.storage.AbstractFileGenomeDescStorage

entries, lastGenomeFile, lastGenomeFileModified, lastMD5Computed

Constructor Summary

Constructors

Modifier	Constructor	Description
protected	DataFileGenomeDescStorage(fr.ens.biologie.genomique.kenetre.storage.DataPath dir, fr.ens.biologie.genomique.kenetre.log.GenericLogger logger)	Protected constructor.

Method Summary

Modifier and Type	Method	Description
protected String	computeMD5Sum(fr.ens.biologie.genomique.kenetre.storage.DataPath genomeFile)
static fr.ens.biologie.genomique.kenetre.storage.GenomeDescStorage	getInstance(DataFile dir, fr.ens.biologie.genomique.kenetre.log.GenericLogger logger)	Create a GenomeDescStorage
protected fr.ens.biologie.genomique.kenetre.storage.DataPath	newDataPath(fr.ens.biologie.genomique.kenetre.storage.DataPath parent, String filename)
protected fr.ens.biologie.genomique.kenetre.storage.DataPath	newDataPath(String source)

Methods inherited from class fr.ens.biologie.genomique.kenetre.storage.AbstractFileGenomeDescStorage

get, put

Methods inherited from class java.lang.Object

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

Constructor Detail

DataFileGenomeDescStorage

protected DataFileGenomeDescStorage(fr.ens.biologie.genomique.kenetre.storage.DataPath dir,
                                    fr.ens.biologie.genomique.kenetre.log.GenericLogger logger)
                             throws IOException

Protected constructor.

Parameters:

dir - directory of the storage.

logger - logger to use

Throws:

IOException - if an error occurs while initializing the object

Method Detail

newDataPath

protected fr.ens.biologie.genomique.kenetre.storage.DataPath newDataPath(String source)

Specified by:

newDataPath in class fr.ens.biologie.genomique.kenetre.storage.AbstractFileGenomeDescStorage

newDataPath

protected fr.ens.biologie.genomique.kenetre.storage.DataPath newDataPath(fr.ens.biologie.genomique.kenetre.storage.DataPath parent,
                                                                         String filename)

Specified by:

newDataPath in class fr.ens.biologie.genomique.kenetre.storage.AbstractFileGenomeDescStorage

computeMD5Sum

protected String computeMD5Sum(fr.ens.biologie.genomique.kenetre.storage.DataPath genomeFile)
                        throws IOException

Overrides:

computeMD5Sum in class fr.ens.biologie.genomique.kenetre.storage.AbstractFileGenomeDescStorage

Throws:

IOException

getInstance

public static fr.ens.biologie.genomique.kenetre.storage.GenomeDescStorage getInstance(DataFile dir,
                                                                                      fr.ens.biologie.genomique.kenetre.log.GenericLogger logger)

Create a GenomeDescStorage

Parameters:

dir - the path of the genome descriptions storage

Returns:

a GenomeDescStorage object if the path contains an index storage or null if no index storage is found