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

Class AbstractSplice2BEDModule

java.lang.Object

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

fr.ens.biologie.genomique.eoulsan.modules.mapping.AbstractSplice2BEDModule

All Implemented Interfaces:

Module

Direct Known Subclasses:

Splice2BEDModule

public abstract class AbstractSplice2BEDModule
extends AbstractModule

This class define a module for converting SAM files into BED.

Since:

2.3

Author:

Laurent Jourdren

Field Summary

Fields

Modifier and Type	Field	Description
protected static String	COUNTER_GROUP

Constructor Summary

Constructors

Constructor	Description
AbstractSplice2BEDModule()

Method Summary

Modifier and Type	Method	Description
void	configure(StepConfigurationContext context, Set<Parameter> stepParameters)	Set the parameters of the step to configure the module.
String	getDescription()	Get the description of the module
InputPorts	getInputPorts()	Get the input data format.
String	getName()	Get the name of the module.
OutputPorts	getOutputPorts()	Get the output data format.
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, getParallelizationMode, getRequiredEoulsanVersion, getRequirements

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

Field Detail

COUNTER_GROUP

protected static final String COUNTER_GROUP

See Also:

Constant Field Values

Constructor Detail

AbstractSplice2BEDModule

public AbstractSplice2BEDModule()

Method Detail

getName

public String getName()

Description copied from interface: Module

Get the name of the module.

Returns:

the name 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

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

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

getOutputPorts

public OutputPorts getOutputPorts()

Description copied from interface: Module

Get the output data format.

Specified by:

getOutputPorts in interface Module

Overrides:

getOutputPorts in class AbstractModule

Returns:

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

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