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

Class DiffAnaModule

java.lang.Object

fr.ens.biologie.genomique.eoulsan.modules.AbstractModule

fr.ens.biologie.genomique.eoulsan.modules.diffana.DiffAnaModule

All Implemented Interfaces:

Module

public class DiffAnaModule
extends AbstractModule

This class define the module of differential analysis in local mode.

Since:

1.0

Author:

Laurent Jourdren, Vivien Deshaies

Constructor Summary

Constructors

Constructor	Description
DiffAnaModule()

Method Summary

Modifier and Type	Method	Description
void	configure(StepConfigurationContext context, Set<Parameter> stepParameters)	Set the parameters of the step to configure the module.
TaskResult	execute(TaskContext context, TaskStatus status)	Execute a task step.
String	getDescription()	Get the description of the module
InputPorts	getInputPorts()	Get the input data format.
String	getName()	Get the name of the module.
Set<Requirement>	getRequirements()	Get the requirements of the module.
fr.ens.biologie.genomique.kenetre.util.Version	getVersion()	Get version of the Module.

Methods inherited from class fr.ens.biologie.genomique.eoulsan.modules.AbstractModule

getChecker, getOutputPorts, getParallelizationMode, getRequiredEoulsanVersion

Methods inherited from class java.lang.Object

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

Constructor Detail

DiffAnaModule

public DiffAnaModule()

Method Detail

getName

public String getName()

Description copied from interface: Module

Get the name of the module.

Returns:

the name of the module

getVersion

public fr.ens.biologie.genomique.kenetre.util.Version getVersion()

Description copied from interface: Module

Get version of the Module.

Returns:

a Version object with the version of the Module

getDescription

public String getDescription()

Description copied from interface: Module

Get the description of the module

Specified by:

getDescription in interface Module

Overrides:

getDescription in class AbstractModule

Returns:

the description of the module

getInputPorts

public InputPorts getInputPorts()

Description copied from interface: Module

Get the input data format.

Specified by:

getInputPorts in interface Module

Overrides:

getInputPorts in class AbstractModule

Returns:

a set with DataFormat or null if the module does not any need input format

getRequirements

public Set<Requirement> getRequirements()

Description copied from interface: Module

Get the requirements of the module.

Specified by:

getRequirements in interface Module

Overrides:

getRequirements in class AbstractModule

Returns:

a set with the requirements of the module

execute

public TaskResult execute(TaskContext context,
                          TaskStatus status)

Description copied from interface: Module

Execute a task step.

Parameters:

context - Execution context

status - of the task

configure

public void configure(StepConfigurationContext context,
                      Set<Parameter> stepParameters)
               throws EoulsanException

Description copied from interface: Module

Set the parameters of the step to configure the module.

Specified by:

configure in interface Module

Overrides:

configure in class AbstractModule

Parameters:

context - configuration context. The context can be null for generator steps

stepParameters - parameters of the step

Throws:

EoulsanException - if a parameter is invalid