Class ExpressionExperimentSubsetValueObject

java.lang.Object

ubic.gemma.model.common.IdentifiableValueObject<ExpressionExperimentSubSet>

ubic.gemma.model.expression.experiment.ExpressionExperimentSubsetValueObject

All Implemented Interfaces:

Serializable, Securable, SecureValueObject, Describable, Identifiable, BioAssaySetValueObject

public class ExpressionExperimentSubsetValueObject
extends IdentifiableValueObject<ExpressionExperimentSubSet>
implements BioAssaySetValueObject

See Also:

• Serialized Form

Field Summary

Fields inherited from class IdentifiableValueObject

id

Constructor Summary

Constructors

Constructor	Description
ExpressionExperimentSubsetValueObject()
ExpressionExperimentSubsetValueObject(ExpressionExperimentSubSet ees)
ExpressionExperimentSubsetValueObject(ExpressionExperimentSubSet ees, Map<ArrayDesign, ArrayDesignValueObject> arrayDesignValueObjectsById, Map<BioAssay,BioAssay> bioAssay2SourceBioAssayMap, boolean includeAssays, boolean basic, boolean allFactorValues)

Method Summary

Modifier and Type	Method	Description
String	getAccession()	Deprecated. Do not use, there's never been an accession field in the data model.
Collection<BioAssayValueObject>	getBioAssays()
Collection<CharacteristicValueObject>	getCharacteristics()
String	getDescription()	Obtain a human-readable description of the object
boolean	getIsPublic()	Indicate if the object is public.
boolean	getIsShared()	Indicate if the object is shared.
Double	getMinPvalue()
String	getName()	Obtain the name of the object.
Integer	getNumberOfBioAssays()	Obtain the number of assays in this set.
Class<? extends Securable>	getSecurableClass()
Long	getSourceExperimentId()	The ID of the ExpressionExperiment this is a subset of.
String	getSourceExperimentShortName()	The short name of the ExpressionExperiment this is a subset of.
boolean	getUserCanWrite()	Indicate if the current user can modify this object.
boolean	getUserOwned()	Indicate if the current user owns the object.
void	setBioAssays(Collection<BioAssayValueObject> bioAssays)
void	setCharacteristics(Collection<CharacteristicValueObject> characteristics)
void	setDescription(String description)
void	setIsPublic(boolean b)
void	setIsShared(boolean b)
void	setMinPvalue(Double minPvalue)
void	setName(String name)
void	setNumberOfBioAssays(Integer numberOfBioAssays)
void	setSourceExperimentId(Long sourceExperimentId)	The ID of the ExpressionExperiment this is a subset of.
void	setSourceExperimentShortName(String sourceExperimentShortName)	The short name of the ExpressionExperiment this is a subset of.
void	setUserCanWrite(boolean userCanWrite)
void	setUserOwned(boolean isUserOwned)

Methods inherited from class IdentifiableValueObject

canEqual, equals, getId, hashCode, setId, toString

Methods inherited from class Object

clone, finalize, getClass, notify, notifyAll, wait, wait, wait

Methods inherited from interface Identifiable

getId

Methods inherited from interface Securable

getId

Constructor Details

ExpressionExperimentSubsetValueObject

public ExpressionExperimentSubsetValueObject()

ExpressionExperimentSubsetValueObject

public ExpressionExperimentSubsetValueObject(ExpressionExperimentSubSet ees)

ExpressionExperimentSubsetValueObject

public ExpressionExperimentSubsetValueObject(ExpressionExperimentSubSet ees,
 @Nullable
 Map<ArrayDesign, ArrayDesignValueObject> arrayDesignValueObjectsById,
 @Nullable
 Map<BioAssay,BioAssay> bioAssay2SourceBioAssayMap,
 boolean includeAssays,
 boolean basic,
 boolean allFactorValues)

Parameters:

bioAssay2SourceBioAssayMap - mapping of assays to their source assays

includeAssays - whether to include assays in the serialization

Method Details

getAccession

@Deprecated
public String getAccession()

Deprecated.

Do not use, there's never been an accession field in the data model.

Always null: a subset has no accession, and never has had one.

Present only because BioAssaySetValueObject.getAccession() declares it. The backing field was removed once it was established that nothing had ever written it — no constructor sets it, and no call site anywhere in the reactor invokes the setter — so the field could only ever have serialized a permanent null. To get a subset's accession, read getSourceExperimentId() and fetch the source experiment.

Specified by:

getAccession in interface BioAssaySetValueObject

getSecurableClass

public Class<? extends Securable> getSecurableClass()

Specified by:

getSecurableClass in interface SecureValueObject

Returns:

the securable Class of the represented entity.

getIsPublic

public boolean getIsPublic()

Description copied from interface: SecureValueObject

Indicate if the object is public.

Specified by:

getIsPublic in interface SecureValueObject

setIsPublic

public void setIsPublic(boolean b)

Specified by:

setIsPublic in interface SecureValueObject

getIsShared

public boolean getIsShared()

Description copied from interface: SecureValueObject

Indicate if the object is shared.

Specified by:

getIsShared in interface SecureValueObject

setIsShared

public void setIsShared(boolean b)

Specified by:

setIsShared in interface SecureValueObject

getUserCanWrite

public boolean getUserCanWrite()

Description copied from interface: SecureValueObject

Indicate if the current user can modify this object.

Specified by:

getUserCanWrite in interface SecureValueObject

setUserCanWrite

public void setUserCanWrite(boolean userCanWrite)

Specified by:

setUserCanWrite in interface SecureValueObject

getUserOwned

public boolean getUserOwned()

Description copied from interface: SecureValueObject

Indicate if the current user owns the object.

Specified by:

getUserOwned in interface SecureValueObject

setUserOwned

public void setUserOwned(boolean isUserOwned)

Specified by:

setUserOwned in interface SecureValueObject

getSourceExperimentId

public Long getSourceExperimentId()

The ID of the ExpressionExperiment this is a subset of.

getSourceExperimentShortName

public String getSourceExperimentShortName()

The short name of the ExpressionExperiment this is a subset of.

getName

public String getName()

Description copied from interface: Describable

Obtain the name of the object.

It may be human-readable.

It is case-insensitive and usually unique within a certain context (e.g. in a collection).

It is non-null by default, but implementation may override this with a Nullable annotation. If null, it should not be treated as equal to other Describable objects (i.e. there can be multiple null-named describable within a given set).

Specified by:

getName in interface Describable

getDescription

public String getDescription()

Description copied from interface: Describable

Obtain a human-readable description of the object

Specified by:

getDescription in interface Describable

getNumberOfBioAssays

public Integer getNumberOfBioAssays()

Description copied from interface: BioAssaySetValueObject

Obtain the number of assays in this set.

Specified by:

getNumberOfBioAssays in interface BioAssaySetValueObject

getCharacteristics

public Collection<CharacteristicValueObject> getCharacteristics()

Specified by:

getCharacteristics in interface BioAssaySetValueObject

getBioAssays

public Collection<BioAssayValueObject> getBioAssays()

getMinPvalue

@Nullable
public Double getMinPvalue()

setSourceExperimentId

public void setSourceExperimentId(Long sourceExperimentId)

The ID of the ExpressionExperiment this is a subset of.

setSourceExperimentShortName

public void setSourceExperimentShortName(String sourceExperimentShortName)

The short name of the ExpressionExperiment this is a subset of.

setName

public void setName(String name)

setDescription

public void setDescription(String description)

setNumberOfBioAssays

public void setNumberOfBioAssays(Integer numberOfBioAssays)

setCharacteristics

public void setCharacteristics(Collection<CharacteristicValueObject> characteristics)

setBioAssays

public void setBioAssays(Collection<BioAssayValueObject> bioAssays)

setMinPvalue

public void setMinPvalue(@Nullable
 Double minPvalue)