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

Class AbstractExpressionModule

java.lang.Object

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

fr.ens.biologie.genomique.eoulsan.modules.expression.AbstractExpressionModule

All Implemented Interfaces:

Module

Direct Known Subclasses:

ExpressionHadoopModule, ExpressionLocalModule

public abstract class AbstractExpressionModule
extends AbstractModule

This abstract class define and parse arguments for the expression module.

Since:

1.0

Author:

Laurent Jourdren, Maria Bernard, Claire Wallon

Field Summary

Fields

Modifier and Type	Field	Description
protected static String	COUNTER_GROUP
static String	COUNTER_PARAMETER_NAME
static String	FEATURES_FILE_FORMAT_PARAMETER_NAME
static String	MODULE_NAME
static String	OUTPUT_FILE_FORMAT_PARAMETER_NAME

Constructor Summary

Constructors

Constructor	Description
AbstractExpressionModule()

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
protected fr.ens.biologie.genomique.kenetre.bio.expressioncounter.ExpressionCounter	getExpressionCounter()	Get the counter.
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.
protected boolean	isGTFInputFormat()	Test if GTF input format must be used.
protected boolean	isSAMOutputFormat()	Test if SAM output format must be used.

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

MODULE_NAME

public static final String MODULE_NAME

See Also:

Constant Field Values

COUNTER_GROUP

protected static final String COUNTER_GROUP

See Also:

Constant Field Values

COUNTER_PARAMETER_NAME

public static final String COUNTER_PARAMETER_NAME

See Also:

Constant Field Values

FEATURES_FILE_FORMAT_PARAMETER_NAME

public static final String FEATURES_FILE_FORMAT_PARAMETER_NAME

See Also:

Constant Field Values

OUTPUT_FILE_FORMAT_PARAMETER_NAME

public static final String OUTPUT_FILE_FORMAT_PARAMETER_NAME

See Also:

Constant Field Values

Constructor Detail

AbstractExpressionModule

public AbstractExpressionModule()

Method Detail

isGTFInputFormat

protected boolean isGTFInputFormat()

Test if GTF input format must be used.

Returns:

true if GTF input format must be used

isSAMOutputFormat

protected boolean isSAMOutputFormat()

Test if SAM output format must be used.

Returns:

true if SAM output format must be used

getExpressionCounter

protected fr.ens.biologie.genomique.kenetre.bio.expressioncounter.ExpressionCounter getExpressionCounter()

Get the counter.

Returns:

the counter

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