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

Class AbstractModule

java.lang.Object

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

All Implemented Interfaces:

Module

Direct Known Subclasses:

AbstractBAM2SAMModule, AbstractExpressionModule, AbstractFilterAndMapReadsModule, AbstractReadsFilterModule, AbstractReadsMapperModule, AbstractSAM2BAMModule, AbstractSAM2FASTQModule, AbstractSAMFilterModule, AbstractSplice2BEDModule, BedToolsModule, CheckerModule, CopyDesignAndWorkflowFilesToOutputModule, CopyInputDataModule, CopyOutputDataModule, CountSplicedReadsModule, DeepToolsModule, DefineDataFormatToDownload, DESeq2Module, DesignModule, DiffAnaModule, DiffanaResultsAnnotationModule, DummyGeneratorModule, ExpressionResultsAnnotationModule, ExpressionToMatrixModule, FailModule, FakeModule, FastQCModule, FirstModule, GalaxyToolModule, GenericStorageGeneratorModule, GenomeDescriptionGeneratorModule, GenomeMapperIndexGeneratorModule, GFFFastaGeneratorModule, HDFSDataDownloadModule, IDRModule, ImportModule, MACS2Module, MatrixToCellRangerMatrixModule, MergeInputRepLocalModule, MergePeaksModule, MergerModule, Minimap2IndexGeneratorModule, MultiQCModule, NormalizationModule, RequirementInstallerModule, RmDupLocalModule, RSingleCellExperimentCreatorModule, ShellModule, SplitterModule, STARIndexGeneratorModule, TerminalModule, TrackHubModule, UploadModule

public abstract class AbstractModule
extends Object
implements Module

This class define an abstract Module.

Since:

1.0

Author:

Laurent Jourdren

Constructor Summary

Constructors

Constructor	Description
AbstractModule()

Method Summary

Modifier and Type	Method	Description
void	configure(StepConfigurationContext context, Set<Parameter> stepParameters)	Set the parameters of the step to configure the module.
Checker	getChecker()	Get the checker for the module
String	getDescription()	Get the description of the module
InputPorts	getInputPorts()	Get the input data format.
OutputPorts	getOutputPorts()	Get the output data format.
ParallelizationMode	getParallelizationMode()	Get the parallelization mode of the module.
fr.ens.biologie.genomique.kenetre.util.Version	getRequiredEoulsanVersion()	Get the required Version of the application to run the Module.
Set<Requirement>	getRequirements()	Get the requirements of the module.

Methods inherited from class java.lang.Object

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

Methods inherited from interface fr.ens.biologie.genomique.eoulsan.core.Module

execute, getName, getVersion

Constructor Detail

AbstractModule

public AbstractModule()

Method Detail

getDescription

public String getDescription()

Description copied from interface: Module

Get the description of the module

Specified by:

getDescription in interface Module

Returns:

the description of the module

getRequiredEoulsanVersion

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

Description copied from interface: Module

Get the required Version of the application to run the Module.

Specified by:

getRequiredEoulsanVersion in interface Module

Returns:

a Version object with the required version of the Module

getInputPorts

public InputPorts getInputPorts()

Description copied from interface: Module

Get the input data format.

Specified by:

getInputPorts in interface Module

Returns:

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

getOutputPorts

public OutputPorts getOutputPorts()

Description copied from interface: Module

Get the output data format.

Specified by:

getOutputPorts in interface Module

Returns:

an set with DataFormat or null if the module does not produce any output data

getRequirements

public Set<Requirement> getRequirements()

Description copied from interface: Module

Get the requirements of the module.

Specified by:

getRequirements in interface Module

Returns:

a set with the requirements of the module

getChecker

public Checker getChecker()

Description copied from interface: Module

Get the checker for the module

Specified by:

getChecker in interface Module

Returns:

the checker for the module

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

Parameters:

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

stepParameters - parameters of the step

Throws:

EoulsanException - if a parameter is invalid

getParallelizationMode

public ParallelizationMode getParallelizationMode()

Description copied from interface: Module

Get the parallelization mode of the module.

Specified by:

getParallelizationMode in interface Module

Returns:

a ParallelizationMode enum