Package ubic.gemma.model.expression.experiment

Class ExpressionExperimentValueObject

java.lang.Object

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

ubic.gemma.model.common.auditAndSecurity.curation.AbstractCuratableValueObject<ExpressionExperiment>

ubic.gemma.model.expression.experiment.ExpressionExperimentValueObject

All Implemented Interfaces:

gemma.gsec.model.Securable, gemma.gsec.model.SecureValueObject, Serializable, Describable, Identifiable, BioAssaySetValueObject

Direct Known Subclasses:

DatasetsWebService.ExpressionExperimentWithSearchResultValueObject, ExpressionExperimentDetailsValueObject

public class ExpressionExperimentValueObject
extends AbstractCuratableValueObject<ExpressionExperiment>
implements BioAssaySetValueObject

See Also:

• Serialized Form

Field Summary

Fields

Modifier and Type	Field	Description
protected String	description
protected String	name
protected Integer	numberOfBioAssays

Fields inherited from class ubic.gemma.model.common.IdentifiableValueObject

id

Constructor Summary

Constructors

Modifier	Constructor	Description
	ExpressionExperimentValueObject()	Required when using the class as a spring bean.
	ExpressionExperimentValueObject(Long id)
	ExpressionExperimentValueObject(ExpressionExperiment ee)
	ExpressionExperimentValueObject(ExpressionExperiment ee, boolean ignoreDesign, boolean ignoreAccession)	Creates a new value object out of given Expression Experiment.
	ExpressionExperimentValueObject(ExpressionExperiment ee, gemma.gsec.acl.domain.AclObjectIdentity aoi, gemma.gsec.acl.domain.AclSid sid)	Creates a new ExpressionExperiment value object with additional information about ownership.
protected	ExpressionExperimentValueObject(ExpressionExperimentValueObject vo)

Method Summary

Modifier and Type	Method	Description
int	getBioAssayCount()	Deprecated. use BioAssaySetValueObject.getNumberOfBioAssays() instead.
boolean	getCurrentUserHasWritePermission()
boolean	getCurrentUserIsOwner()
boolean	getIsPublic()
boolean	getIsShared()
Class<? extends Securable>	getSecurableClass()
String	getTaxon()
Long	getTaxonId()	Deprecated. use invalid reference #getTaxonObject() instead
boolean	getUserCanWrite()
boolean	getUserOwned()
void	setIsPublic(boolean b)
void	setIsShared(boolean b)
void	setUserCanWrite(boolean userCanWrite)
void	setUserOwned(boolean isUserOwned)
String	toString()

Methods inherited from class ubic.gemma.model.common.auditAndSecurity.curation.AbstractCuratableValueObject

getCurationNote, getLastNeedsAttentionEvent, getLastNoteUpdateEvent, getLastTroubledEvent, getLastUpdated, getNeedsAttention, getTroubled, getTroubleDetails, getTroubleDetails, setCurationNote, setLastNeedsAttentionEvent, setLastNoteUpdateEvent, setLastTroubledEvent, setLastUpdated, setNeedsAttention, setTroubled

Methods inherited from class ubic.gemma.model.common.IdentifiableValueObject

getId, setId

Methods inherited from class java.lang.Object

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

Methods inherited from interface ubic.gemma.model.expression.experiment.BioAssaySetValueObject

getAccession, getCharacteristics, getNumberOfBioAssays

Methods inherited from interface ubic.gemma.model.common.Describable

getDescription, getName

Methods inherited from interface ubic.gemma.model.common.Identifiable

getId

Methods inherited from interface gemma.gsec.model.Securable

getId

Field Details

numberOfBioAssays

protected Integer numberOfBioAssays

description

protected String description

name

protected String name

Constructor Details

ExpressionExperimentValueObject

public ExpressionExperimentValueObject()

Required when using the class as a spring bean.

ExpressionExperimentValueObject

public ExpressionExperimentValueObject(Long id)

ExpressionExperimentValueObject

public ExpressionExperimentValueObject(ExpressionExperiment ee,
 boolean ignoreDesign,
 boolean ignoreAccession)

Creates a new value object out of given Expression Experiment.

Parameters:

ee - the experiment to convert into a value object.

ignoreDesign - exclude the experimental design from serialization

ignoreAccession - exclude accession from serialization

ExpressionExperimentValueObject

public ExpressionExperimentValueObject(ExpressionExperiment ee)

ExpressionExperimentValueObject

public ExpressionExperimentValueObject(ExpressionExperiment ee,
 gemma.gsec.acl.domain.AclObjectIdentity aoi,
 gemma.gsec.acl.domain.AclSid sid)

Creates a new ExpressionExperiment value object with additional information about ownership.

ExpressionExperimentValueObject

protected ExpressionExperimentValueObject(ExpressionExperimentValueObject vo)

Method Details

getBioAssayCount

@Deprecated
public int getBioAssayCount()

Deprecated.

use BioAssaySetValueObject.getNumberOfBioAssays() instead.

Obtain the number of BioAssay in this experiment.

getIsPublic

public boolean getIsPublic()

Specified by:

getIsPublic in interface gemma.gsec.model.SecureValueObject

getIsShared

public boolean getIsShared()

Specified by:

getIsShared in interface gemma.gsec.model.SecureValueObject

getTaxon

public String getTaxon()

getTaxonId

@Deprecated
public Long getTaxonId()

Deprecated.

use

invalid reference

#getTaxonObject()

instead

getSecurableClass

public Class<? extends Securable> getSecurableClass()

Specified by:

getSecurableClass in interface gemma.gsec.model.SecureValueObject

getUserCanWrite

public boolean getUserCanWrite()

Specified by:

getUserCanWrite in interface gemma.gsec.model.SecureValueObject

getUserOwned

public boolean getUserOwned()

Specified by:

getUserOwned in interface gemma.gsec.model.SecureValueObject

setIsPublic

public void setIsPublic(boolean b)

Specified by:

setIsPublic in interface gemma.gsec.model.SecureValueObject

setIsShared

public void setIsShared(boolean b)

Specified by:

setIsShared in interface gemma.gsec.model.SecureValueObject

setUserCanWrite

public void setUserCanWrite(boolean userCanWrite)

Specified by:

setUserCanWrite in interface gemma.gsec.model.SecureValueObject

setUserOwned

public void setUserOwned(boolean isUserOwned)

Specified by:

setUserOwned in interface gemma.gsec.model.SecureValueObject

getCurrentUserHasWritePermission

public boolean getCurrentUserHasWritePermission()

getCurrentUserIsOwner

public boolean getCurrentUserIsOwner()

toString

public String toString()

Overrides:

toString in class IdentifiableValueObject<ExpressionExperiment>