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

Class UnmodifiableExperimentMetadata

java.lang.Object

fr.ens.biologie.genomique.eoulsan.design.UnmodifiableExperimentMetadata

All Implemented Interfaces:

ExperimentMetadata, Metadata, Serializable

public class UnmodifiableExperimentMetadata
extends Object
implements ExperimentMetadata, Serializable

See Also:

• Serialized Form

Field Summary

Fields inherited from interface fr.ens.biologie.genomique.eoulsan.design.ExperimentMetadata

BUILD_CONTRAST_KEY, COMPARISONS_KEY, CONTRAST_FILE_KEY, CONTRAST_KEY, DESIGN_FILE_KEY, MODEL_KEY, REFERENCE_KEY, SKIP_KEY

Method Summary

Modifier and Type	Method	Description
boolean	contains(String key)	Test if the key is in md.
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.
Set<Map.Entry<String,String>>	entrySet()	Get an entry set of the metadata.
boolean	equals(Object obj)
String	get(String key)	Get the value according the key.
boolean	getAsBoolean(String key)	Get the value according the key as a boolean.
List<String>	getAsList(String key)	Get the value according the key as a list.
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.
String	getTrimmed(String key)	Get the trimmed value according the key.
int	hashCode()
boolean	isBuildContrast()	Get the buildContrast DEseq2 option.
boolean	isContrast()	Get the contrast DEseq2 option.
boolean	isEmpty()	Test if there is no metadata.
boolean	isSkip()	Get the skip option.
Set<String>	keySet()	Get the keys of the metadata
void	remove(String key)	Remove the value according the key.
void	set(String key, String value)	Set the value according the key.
void	set(String key, List<String> value)	Set the value as a list according the key.
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.
int	size()	Get the number of metadata.

Methods inherited from class java.lang.Object

getClass, notify, notifyAll, toString, wait, wait, wait

Method Details

get

public String get(String key)

Description copied from interface: Metadata

Get the value according the key.

Specified by:

get in interface Metadata

Parameters:

key - the key

Returns:

the value

getTrimmed

public String getTrimmed(String key)

Description copied from interface: Metadata

Get the trimmed value according the key.

Specified by:

getTrimmed in interface Metadata

Parameters:

key - the key

Returns:

the value

set

public void set(String key,
 String value)

Description copied from interface: Metadata

Set the value according the key.

Specified by:

set in interface Metadata

Parameters:

key - the key

value - the value

set

public void set(String key,
 List<String> value)

Description copied from interface: Metadata

Set the value as a list according the key.

Specified by:

set in interface Metadata

Parameters:

key - the key

value - the value as a list

size

public int size()

Description copied from interface: Metadata

Get the number of metadata.

Specified by:

size in interface Metadata

Returns:

the number of metadata

isEmpty

public boolean isEmpty()

Description copied from interface: Metadata

Test if there is no metadata.

Specified by:

isEmpty in interface Metadata

Returns:

true if there is no metadata

contains

public boolean contains(String key)

Description copied from interface: Metadata

Test if the key is in md.

Specified by:

contains in interface Metadata

Parameters:

key - the key

Returns:

true if the key is in md

getAsList

public List<String> getAsList(String key)

Description copied from interface: Metadata

Get the value according the key as a list.

Specified by:

getAsList in interface Metadata

Parameters:

key - the key

Returns:

the value as a list

getAsBoolean

public boolean getAsBoolean(String key)

Description copied from interface: Metadata

Get the value according the key as a boolean.

Specified by:

getAsBoolean in interface Metadata

Parameters:

key - the key

Returns:

the value as a boolean

keySet

public Set<String> keySet()

Description copied from interface: Metadata

Get the keys of the metadata

Specified by:

keySet in interface Metadata

Returns:

a set with the keys of the metadata

entrySet

public Set<Map.Entry<String,String>> entrySet()

Description copied from interface: Metadata

Get an entry set of the metadata.

Specified by:

entrySet in interface Metadata

Returns:

a set of entries

remove

public void remove(String key)

Description copied from interface: Metadata

Remove the value according the key.

Specified by:

remove in interface Metadata

Parameters:

key - the key

isSkip

public boolean isSkip()

Description copied from interface: ExperimentMetadata

Get the skip option.

Specified by:

isSkip in interface ExperimentMetadata

Returns:

the skip option

getReference

public String getReference()

Description copied from interface: ExperimentMetadata

Get the reference option.

Specified by:

getReference in interface ExperimentMetadata

Returns:

the reference option

getModel

public String getModel()

Description copied from interface: ExperimentMetadata

Get the model DEseq2 option.

Specified by:

getModel in interface ExperimentMetadata

Returns:

the model DEseq2 option

isContrast

public boolean isContrast()

Description copied from interface: ExperimentMetadata

Get the contrast DEseq2 option.

Specified by:

isContrast in interface ExperimentMetadata

Returns:

the contrast DEseq2 option

isBuildContrast

public boolean isBuildContrast()

Description copied from interface: ExperimentMetadata

Get the buildContrast DEseq2 option.

Specified by:

isBuildContrast in interface ExperimentMetadata

Returns:

the buildContrast DEseq2 option

getDesignFile

public String getDesignFile()

Description copied from interface: ExperimentMetadata

Get the designFile DEseq2 option.

Specified by:

getDesignFile in interface ExperimentMetadata

Returns:

the designFile DEseq2 option

getComparisons

public String getComparisons()

Description copied from interface: ExperimentMetadata

Get the comparisons DEseq2 option.

Specified by:

getComparisons in interface ExperimentMetadata

Returns:

the comparisons DEseq2 option

getContrastFile

public String getContrastFile()

Description copied from interface: ExperimentMetadata

Get the contrastFile DEseq2 option.

Specified by:

getContrastFile in interface ExperimentMetadata

Returns:

the contrastFile DEseq2 option

setSkip

public void setSkip(boolean newSkip)

Description copied from interface: ExperimentMetadata

Set the skip option.

Specified by:

setSkip in interface ExperimentMetadata

Parameters:

newSkip - the new skip option

setReference

public void setReference(String newReference)

Description copied from interface: ExperimentMetadata

Set the reference option.

Specified by:

setReference in interface ExperimentMetadata

Parameters:

newReference - the new reference option

setModel

public void setModel(String newModel)

Description copied from interface: ExperimentMetadata

Set the model DEseq2 option.

Specified by:

setModel in interface ExperimentMetadata

Parameters:

newModel - the new model DEseq2 option

setContrast

public void setContrast(boolean newContrast)

Description copied from interface: ExperimentMetadata

Set the contrast DEseq2 option.

Specified by:

setContrast in interface ExperimentMetadata

Parameters:

newContrast - the new contrast DEseq2 option

setBuildContrast

public void setBuildContrast(boolean newBuildContrast)

Description copied from interface: ExperimentMetadata

Set the buildContrast DEseq2 option.

Specified by:

setBuildContrast in interface ExperimentMetadata

Parameters:

newBuildContrast - the new buildContrast DEseq2 option

setDesignFile

public void setDesignFile(String newDesignFile)

Description copied from interface: ExperimentMetadata

Set the designFile DEseq2 option.

Specified by:

setDesignFile in interface ExperimentMetadata

Parameters:

newDesignFile - the new designFile DEseq2 option

setComparisons

public void setComparisons(String newComparisons)

Description copied from interface: ExperimentMetadata

Set the comparisons DEseq2 option.

Specified by:

setComparisons in interface ExperimentMetadata

Parameters:

newComparisons - the new comparisons DEseq2 option

setContrastFile

public void setContrastFile(String newContrastFile)

Description copied from interface: ExperimentMetadata

Set the contrastFile DEseq2 option.

Specified by:

setContrastFile in interface ExperimentMetadata

Parameters:

newContrastFile - the new contrastFile DEseq2 option

containsSkip

public boolean containsSkip()

Description copied from interface: ExperimentMetadata

Test if the skip option exists.

Specified by:

containsSkip in interface ExperimentMetadata

Returns:

true if the skip option exists

containsReference

public boolean containsReference()

Description copied from interface: ExperimentMetadata

Test if the reference option exists.

Specified by:

containsReference in interface ExperimentMetadata

Returns:

true if the reference option exists

containsModel

public boolean containsModel()

Description copied from interface: ExperimentMetadata

Test if the model option exists.

Specified by:

containsModel in interface ExperimentMetadata

Returns:

true if the model option exists

containsContrast

public boolean containsContrast()

Description copied from interface: ExperimentMetadata

Test if the contrast option exists.

Specified by:

containsContrast in interface ExperimentMetadata

Returns:

true if the contrast option exists

containsBuildContrast

public boolean containsBuildContrast()

Description copied from interface: ExperimentMetadata

Test if the buildContrast option exists.

Specified by:

containsBuildContrast in interface ExperimentMetadata

Returns:

true if the buildContrast option exists

containsDesignFile

public boolean containsDesignFile()

Description copied from interface: ExperimentMetadata

Test if the designFile option exists.

Specified by:

containsDesignFile in interface ExperimentMetadata

Returns:

true if the designFile option exists

containsComparisons

public boolean containsComparisons()

Description copied from interface: ExperimentMetadata

Test if the comparisons option exists.

Specified by:

containsComparisons in interface ExperimentMetadata

Returns:

true if the comparisons option exists

containsContrastFile

public boolean containsContrastFile()

Description copied from interface: ExperimentMetadata

Test if the contrastFile option exists.

Specified by:

containsContrastFile in interface ExperimentMetadata

Returns:

true if the contrastFile option exists

hashCode

public int hashCode()

Overrides:

hashCode in class Object

equals

public boolean equals(Object obj)

Overrides:

equals in class Object