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

Class AbstractReadsMapperModule

java.lang.Object

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

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

All Implemented Interfaces:

Module

Direct Known Subclasses:

ReadsMapperHadoopModule, ReadsMapperLocalModule

public abstract class AbstractReadsMapperModule
extends AbstractModule

This class define an abstract module for read mapping.

Since:

1.0

Author:

Laurent Jourdren

Field Summary

Fields

Modifier and Type	Field	Description
static final String	HADOOP_THREADS_PARAMETER_NAME
static final int	HADOOP_TIMEOUT
static final String	LOCAL_THREADS_PARAMETER_NAME
static final String	MAPPER_ARGUMENTS_PARAMETER_NAME
static final String	MAPPER_DOCKER_IMAGE_PARAMETER_NAME
static final String	MAPPER_FLAVOR_PARAMETER_NAME
static final String	MAPPER_NAME_PARAMETER_NAME
static final String	MAPPER_VERSION_PARAMETER_NAME
static final String	MAX_LOCAL_THREADS_PARAMETER_NAME
static final String	MODULE_NAME	Module name.
static final String	USE_BUNDLED_BINARIES_PARAMETER_NAME

Constructor Summary

Constructors

Constructor	Description
AbstractReadsMapperModule()

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
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, getInputPorts, getParallelizationMode, getRequiredEoulsanVersion, getRequirements

Methods inherited from class java.lang.Object

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

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

execute

Field Details

MODULE_NAME

public static final String MODULE_NAME

Module name.

See Also:

• Constant Field Values

MAPPER_NAME_PARAMETER_NAME

public static final String MAPPER_NAME_PARAMETER_NAME

See Also:

• Constant Field Values

MAPPER_VERSION_PARAMETER_NAME

public static final String MAPPER_VERSION_PARAMETER_NAME

See Also:

• Constant Field Values

MAPPER_FLAVOR_PARAMETER_NAME

public static final String MAPPER_FLAVOR_PARAMETER_NAME

See Also:

• Constant Field Values

USE_BUNDLED_BINARIES_PARAMETER_NAME

public static final String USE_BUNDLED_BINARIES_PARAMETER_NAME

See Also:

• Constant Field Values

MAPPER_DOCKER_IMAGE_PARAMETER_NAME

public static final String MAPPER_DOCKER_IMAGE_PARAMETER_NAME

See Also:

• Constant Field Values

MAPPER_ARGUMENTS_PARAMETER_NAME

public static final String MAPPER_ARGUMENTS_PARAMETER_NAME

See Also:

• Constant Field Values

HADOOP_THREADS_PARAMETER_NAME

public static final String HADOOP_THREADS_PARAMETER_NAME

See Also:

• Constant Field Values

LOCAL_THREADS_PARAMETER_NAME

public static final String LOCAL_THREADS_PARAMETER_NAME

See Also:

• Constant Field Values

MAX_LOCAL_THREADS_PARAMETER_NAME

public static final String MAX_LOCAL_THREADS_PARAMETER_NAME

See Also:

• Constant Field Values

HADOOP_TIMEOUT

public static final int HADOOP_TIMEOUT

See Also:

• Constant Field Values

Constructor Details

AbstractReadsMapperModule

public AbstractReadsMapperModule()

Method Details

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

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