Package fr.ens.biologie.genomique.eoulsan.modules.generators

Class GenomeDescriptionCreator

java.lang.Object

fr.ens.biologie.genomique.eoulsan.modules.generators.GenomeDescriptionCreator

public class GenomeDescriptionCreator
extends Object

This class define a genome description creator.

Since:

1.2

Author:

Laurent Jourdren

Constructor Summary

Constructors

Constructor	Description
GenomeDescriptionCreator()	Public constructor.

Method Summary

Modifier and Type	Method	Description
fr.ens.biologie.genomique.kenetre.bio.GenomeDescription	createGenomeDescription(DataFile genomeDataFile)	Create genome description object from the storage if already exists or compute it from the genome.
fr.ens.biologie.genomique.kenetre.bio.GenomeDescription	createGenomeDescriptionFromAnnotation(DataFile annotationDataFile)	Create genome description object from the storage if already exists or compute it from the genome.

Methods inherited from class java.lang.Object

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

Constructor Detail

GenomeDescriptionCreator

public GenomeDescriptionCreator()

Public constructor.

Method Detail

createGenomeDescriptionFromAnnotation

public fr.ens.biologie.genomique.kenetre.bio.GenomeDescription createGenomeDescriptionFromAnnotation(DataFile annotationDataFile)
                                                                                              throws fr.ens.biologie.genomique.kenetre.bio.BadBioEntryException,
                                                                                                     IOException

Create genome description object from the storage if already exists or compute it from the genome.

Parameters:

annotationDataFile - annotation file

Returns:

the genome description object

Throws:

fr.ens.biologie.genomique.kenetre.bio.BadBioEntryException - if an error occurs while computing the genome description

IOException - if an error occurs while computing the genome description

createGenomeDescription

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

Create genome description object from the storage if already exists or compute it from the genome.

Parameters:

genomeDataFile - genome file

Returns:

the genome description object

Throws:

fr.ens.biologie.genomique.kenetre.bio.BadBioEntryException - if an error occurs while computing the genome description

IOException - if an error occurs while computing the genome description