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

Class GFFChecker

java.lang.Object

fr.ens.biologie.genomique.eoulsan.checkers.GFFChecker

All Implemented Interfaces:

Checker

Direct Known Subclasses:

GTFChecker

public class GFFChecker
extends Object
implements Checker

This class define a Checker on GFF annotation.

Since:

1.0

Author:

Laurent Jourdren

Constructor Summary

Constructors

Modifier	Constructor	Description
	GFFChecker()	Public constructor.
protected	GFFChecker(boolean gtfFormat)	Protected constructor.

Method Summary

Modifier and Type	Method	Description
boolean	check(Data data, CheckStore checkInfo)	Launch the check.
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

GFFChecker

protected GFFChecker(boolean gtfFormat)

Protected constructor.

Parameters:

gtfFormat - true if the format the file is GTF

GFFChecker

public GFFChecker()

Public constructor.

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

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

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