Package fr.ens.biologie.genomique.eoulsan.design

Interface ExperimentMetadata

All Superinterfaces:

Metadata

All Known Implementing Classes:

UnmodifiableExperimentMetadata

public interface ExperimentMetadata
extends Metadata

This interface defines the experiment metadata.

Since:

2.0

Author:

Xavier Bauquet

Field Summary

Fields

Modifier and Type	Field	Description
static String	BUILD_CONTRAST_KEY
static String	COMPARISONS_KEY
static String	CONTRAST_FILE_KEY
static String	CONTRAST_KEY
static String	DESIGN_FILE_KEY
static String	MODEL_KEY
static String	REFERENCE_KEY
static String	SKIP_KEY

Method Summary

Modifier and Type	Method	Description
boolean	containsBuildContrast()	Test if the buildContrast option exists.
boolean	containsComparisons()	Test if the comparisons option exists.
boolean	containsContrast()	Test if the contrast option exists.
boolean	containsContrastFile()	Test if the contrastFile option exists.
boolean	containsDesignFile()	Test if the designFile option exists.
boolean	containsModel()	Test if the model option exists.
boolean	containsReference()	Test if the reference option exists.
boolean	containsSkip()	Test if the skip option exists.
String	getComparisons()	Get the comparisons DEseq2 option.
String	getContrastFile()	Get the contrastFile DEseq2 option.
String	getDesignFile()	Get the designFile DEseq2 option.
String	getModel()	Get the model DEseq2 option.
String	getReference()	Get the reference option.
boolean	isBuildContrast()	Get the buildContrast DEseq2 option.
boolean	isContrast()	Get the contrast DEseq2 option.
boolean	isSkip()	Get the skip option.
void	setBuildContrast(boolean newBuildContrast)	Set the buildContrast DEseq2 option.
void	setComparisons(String newComparisons)	Set the comparisons DEseq2 option.
void	setContrast(boolean newContrast)	Set the contrast DEseq2 option.
void	setContrastFile(String newContrastFile)	Set the contrastFile DEseq2 option.
void	setDesignFile(String newDesignFile)	Set the designFile DEseq2 option.
void	setModel(String newModel)	Set the model DEseq2 option.
void	setReference(String newReference)	Set the reference option.
void	setSkip(boolean newSkip)	Set the skip option.

Methods inherited from interface fr.ens.biologie.genomique.eoulsan.design.Metadata

contains, entrySet, equals, get, getAsBoolean, getAsList, getTrimmed, isEmpty, keySet, remove, set, set, size

Field Detail

SKIP_KEY

static final String SKIP_KEY

See Also:

Constant Field Values

REFERENCE_KEY

static final String REFERENCE_KEY

See Also:

Constant Field Values

MODEL_KEY

static final String MODEL_KEY

See Also:

Constant Field Values

CONTRAST_KEY

static final String CONTRAST_KEY

See Also:

Constant Field Values

BUILD_CONTRAST_KEY

static final String BUILD_CONTRAST_KEY

See Also:

Constant Field Values

DESIGN_FILE_KEY

static final String DESIGN_FILE_KEY

See Also:

Constant Field Values

COMPARISONS_KEY

static final String COMPARISONS_KEY

See Also:

Constant Field Values

CONTRAST_FILE_KEY

static final String CONTRAST_FILE_KEY

See Also:

Constant Field Values

Method Detail

isSkip

boolean isSkip()

Get the skip option.

Returns:

the skip option

getReference

String getReference()

Get the reference option.

Returns:

the reference option

getModel

String getModel()

Get the model DEseq2 option.

Returns:

the model DEseq2 option

isContrast

boolean isContrast()

Get the contrast DEseq2 option.

Returns:

the contrast DEseq2 option

isBuildContrast

boolean isBuildContrast()

Get the buildContrast DEseq2 option.

Returns:

the buildContrast DEseq2 option

getDesignFile

String getDesignFile()

Get the designFile DEseq2 option.

Returns:

the designFile DEseq2 option

getComparisons

String getComparisons()

Get the comparisons DEseq2 option.

Returns:

the comparisons DEseq2 option

getContrastFile

String getContrastFile()

Get the contrastFile DEseq2 option.

Returns:

the contrastFile DEseq2 option

setSkip

void setSkip(boolean newSkip)

Set the skip option.

Parameters:

newSkip - the new skip option

setReference

void setReference(String newReference)

Set the reference option.

Parameters:

newReference - the new reference option

setModel

void setModel(String newModel)

Set the model DEseq2 option.

Parameters:

newModel - the new model DEseq2 option

setContrast

void setContrast(boolean newContrast)

Set the contrast DEseq2 option.

Parameters:

newContrast - the new contrast DEseq2 option

setBuildContrast

void setBuildContrast(boolean newBuildContrast)

Set the buildContrast DEseq2 option.

Parameters:

newBuildContrast - the new buildContrast DEseq2 option

setDesignFile

void setDesignFile(String newDesignFile)

Set the designFile DEseq2 option.

Parameters:

newDesignFile - the new designFile DEseq2 option

setComparisons

void setComparisons(String newComparisons)

Set the comparisons DEseq2 option.

Parameters:

newComparisons - the new comparisons DEseq2 option

setContrastFile

void setContrastFile(String newContrastFile)

Set the contrastFile DEseq2 option.

Parameters:

newContrastFile - the new contrastFile DEseq2 option

containsSkip

boolean containsSkip()

Test if the skip option exists.

Returns:

true if the skip option exists

containsReference

boolean containsReference()

Test if the reference option exists.

Returns:

true if the reference option exists

containsModel

boolean containsModel()

Test if the model option exists.

Returns:

true if the model option exists

containsContrast

boolean containsContrast()

Test if the contrast option exists.

Returns:

true if the contrast option exists

containsBuildContrast

boolean containsBuildContrast()

Test if the buildContrast option exists.

Returns:

true if the buildContrast option exists

containsDesignFile

boolean containsDesignFile()

Test if the designFile option exists.

Returns:

true if the designFile option exists

containsComparisons

boolean containsComparisons()

Test if the comparisons option exists.

Returns:

true if the comparisons option exists

containsContrastFile

boolean containsContrastFile()

Test if the contrastFile option exists.

Returns:

true if the contrastFile option exists