Package fr.ens.biologie.genomique.aozan.fastqscreen

Class GenomeAliases

java.lang.Object

fr.ens.biologie.genomique.aozan.fastqscreen.GenomeAliases

public class GenomeAliases
extends Object

This class define a storage for genome name aliases.

Author:

Laurent Jourdren, Sandrine Perrin

Method Summary

Modifier and Type	Method	Description
void	addAlias(String genomeName, String alias)	Add an alias.
void	addUnknownAlias(String genomeName)	Add an alias.
boolean	contains(String genomeName)
String	get(String genomeName)	Return the reference genome corresponding to the genome sample if it is present in alias genomes file.
static GenomeAliases	getInstance()	Create a instance of GenomeAliases or if it exists return instance.
static void	initialize(Settings settings)	Create a instance of GenomeAliases or if it exists return instance.
void	saveUnknownAliases()	Add the genome of the sample in the file which does correspondence with reference genome.

Methods inherited from class java.lang.Object

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

Method Detail

get

public String get(String genomeName)

Return the reference genome corresponding to the genome sample if it is present in alias genomes file.

Parameters:

genomeName - name of genome sample

Returns:

reference genome corresponding to genome if it exists or empty string or null if no genome exist.

contains

public boolean contains(String genomeName)

addAlias

public void addAlias(String genomeName,
                     String alias)

Add an alias.

Parameters:

genomeName - alias

alias - the value of the alias

addUnknownAlias

public void addUnknownAlias(String genomeName)

Add an alias.

Parameters:

genomeName - the name of the unknown alias

saveUnknownAliases

public void saveUnknownAliases()

Add the genome of the sample in the file which does correspondence with reference genome.

initialize

public static void initialize(Settings settings)
                       throws AozanException

Create a instance of GenomeAliases or if it exists return instance.

Parameters:

settings - Aozan settings

Throws:

AozanException - if the initialization of instance fail.

getInstance

public static GenomeAliases getInstance()
                                 throws AozanException

Create a instance of GenomeAliases or if it exists return instance.

Returns:

instance of GenomeAliases

Throws:

AozanException - if the instance doesn't exist