Package fr.ens.biologie.genomique.eoulsan.checkers

Class DESeq2DesignChecker

java.lang.Object

fr.ens.biologie.genomique.eoulsan.checkers.DESeq2DesignChecker

All Implemented Interfaces:

Checker, Serializable

public class DESeq2DesignChecker
extends Object
implements Checker, Serializable

This class define a Checker on the design for DESeq2 analyzes.

Since:

2.4

Author:

Charlotte Berthelier

See Also:

Serialized Form

Constructor Summary

Constructors

Constructor	Description
DESeq2DesignChecker()

Method Summary

Modifier and Type	Method	Description
boolean	check(Data data, CheckStore checkInfo)	Launch the check.
static boolean	checkExperimentDesign(Experiment experiment)	Check experiment design.
void	configure(Set<Parameter> stepParameters)	Set the parameters of the checker to configure the checker.
Set<DataFormat>	getCheckersRequired()	Get the list of Checker required to run before this checker.
DataFormat	getFormat()	Get format related to the checker.
String	getName()	Get the name of the checker.
boolean	isDesignChecker()	Test if the Checker is a design checker

Methods inherited from class java.lang.Object

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

Constructor Detail

DESeq2DesignChecker

public DESeq2DesignChecker()

Method Detail

getName

public String getName()

Description copied from interface: Checker

Get the name of the checker.

Specified by:

getName in interface Checker

Returns:

the name of the checker

isDesignChecker

public boolean isDesignChecker()

Description copied from interface: Checker

Test if the Checker is a design checker

Specified by:

isDesignChecker in interface Checker

getFormat

public DataFormat getFormat()

Description copied from interface: Checker

Get format related to the checker.

Specified by:

getFormat in interface Checker

Returns:

a DataFormat object

configure

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

Description copied from interface: Checker

Set the parameters of the checker to configure the checker.

Specified by:

configure in interface Checker

Parameters:

stepParameters - parameters of the step

Throws:

EoulsanException - if a parameter is invalid

check

public boolean check(Data data,
                     CheckStore checkInfo)
              throws EoulsanException

Description copied from interface: Checker

Launch the check.

Specified by:

check in interface Checker

Parameters:

data - data to check

checkInfo - object that contains data shared between the checkers

Throws:

EoulsanException - if an error occurs while executing step

getCheckersRequired

public Set<DataFormat> getCheckersRequired()

Description copied from interface: Checker

Get the list of Checker required to run before this checker.

Specified by:

getCheckersRequired in interface Checker

Returns:

a list of DataFormat that are checked by the required checkers

checkExperimentDesign

public static boolean checkExperimentDesign(Experiment experiment)
                                     throws EoulsanException

Check experiment design.

Parameters:

experiment - experiment to check

Throws:

EoulsanException - if the experiment design is not correct