Package ubic.gemma.model.expression.experiment

Class ExpressionExperimentDetailsValueObject

java.lang.Object

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

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

ubic.gemma.model.expression.experiment.ExpressionExperimentValueObject

ubic.gemma.model.expression.experiment.ExpressionExperimentDetailsValueObject

All Implemented Interfaces:

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

Direct Known Subclasses:

ExpressionExperimentEditValueObject

public class ExpressionExperimentDetailsValueObject
extends ExpressionExperimentValueObject

Author:

paul

See Also:

Serialized Form

Field Summary

Fields inherited from class ubic.gemma.model.expression.experiment.ExpressionExperimentValueObject

description, name, numberOfBioAssays

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

id

Constructor Summary

Constructors

Constructor	Description
ExpressionExperimentDetailsValueObject()	Required when using the class as a spring bean.
ExpressionExperimentDetailsValueObject(ExpressionExperiment ee)
ExpressionExperimentDetailsValueObject(ExpressionExperiment ee, gemma.gsec.acl.domain.AclObjectIdentity aoi, gemma.gsec.acl.domain.AclSid sid)
ExpressionExperimentDetailsValueObject(ExpressionExperimentValueObject vo)

Method Summary

Modifier and Type	Method	Description
boolean	getActuallyTroubled()
boolean	getHasBatchInformation()
boolean	getHasBothIntensities()
boolean	getHasCoexpressionAnalysis()
boolean	getHasDifferentialExpressionAnalysis()
boolean	getHasEitherIntensity()
boolean	getHasMultiplePreferredQuantitationTypes()
boolean	getHasMultipleTechnologyTypes()
boolean	getIsRNASeq()
boolean	getIsSingleCell()
Boolean	getPlatformTroubled()
boolean	getReprocessedFromRawData()
boolean	getTroubled()
String	getTroubleDetails()
String	getTroubleDetails(boolean htmlEscape)	Checks trouble of this EE and all its Array Designs and returns compilation of trouble info.
void	setArrayDesigns(Collection<ArrayDesignValueObject> arrayDesigns)	As a side effect, sets the technology type and taxon of this based on the first arrayDesign.
void	setIsRNASeq(boolean isRNASeq)
void	setIsSingleCell(boolean isSingleCell)

Methods inherited from class ubic.gemma.model.expression.experiment.ExpressionExperimentValueObject

getBioAssayCount, getCurrentUserHasWritePermission, getCurrentUserIsOwner, getIsPublic, getIsShared, getSecurableClass, getTaxon, getTaxonId, getUserCanWrite, getUserOwned, setIsPublic, setIsShared, setUserCanWrite, setUserOwned, toString

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

getNeedsAttention

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

Constructor Detail

ExpressionExperimentDetailsValueObject

public ExpressionExperimentDetailsValueObject()

Required when using the class as a spring bean.

ExpressionExperimentDetailsValueObject

public ExpressionExperimentDetailsValueObject(ExpressionExperiment ee)

ExpressionExperimentDetailsValueObject

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

ExpressionExperimentDetailsValueObject

public ExpressionExperimentDetailsValueObject(ExpressionExperimentValueObject vo)

Method Detail

getActuallyTroubled

public boolean getActuallyTroubled()

Returns:

true if this EE is troubled, disregards any platform trouble that might be present.

getHasBatchInformation

public boolean getHasBatchInformation()

getHasBothIntensities

public boolean getHasBothIntensities()

getHasCoexpressionAnalysis

public boolean getHasCoexpressionAnalysis()

getHasDifferentialExpressionAnalysis

public boolean getHasDifferentialExpressionAnalysis()

getHasEitherIntensity

public boolean getHasEitherIntensity()

getHasMultiplePreferredQuantitationTypes

public boolean getHasMultiplePreferredQuantitationTypes()

getHasMultipleTechnologyTypes

public boolean getHasMultipleTechnologyTypes()

getIsSingleCell

public boolean getIsSingleCell()

setIsSingleCell

public void setIsSingleCell(boolean isSingleCell)

getIsRNASeq

public boolean getIsRNASeq()

setIsRNASeq

public void setIsRNASeq(boolean isRNASeq)

getPlatformTroubled

@Nullable
public Boolean getPlatformTroubled()

Returns:

true, if the any of the platforms of this EE is troubled. False otherwise, even if this EE itself is troubled. May return null if the arrayDesigns are not set.

getReprocessedFromRawData

public boolean getReprocessedFromRawData()

getTroubled

public boolean getTroubled()

Overrides:

getTroubled in class AbstractCuratableValueObject<ExpressionExperiment>

Returns:

true if the EE, or any of its Array Designs is troubled.

getTroubleDetails

public String getTroubleDetails()

Overrides:

getTroubleDetails in class AbstractCuratableValueObject<ExpressionExperiment>

Returns:

html-escaped string with trouble info.

See Also:

getTroubleDetails(boolean)

getTroubleDetails

public String getTroubleDetails(boolean htmlEscape)

Checks trouble of this EE and all its Array Designs and returns compilation of trouble info. MAKE SURE to fill the Array Design variable first!

Overrides:

getTroubleDetails in class AbstractCuratableValueObject<ExpressionExperiment>

Parameters:

htmlEscape - whether to escape the returned string for html

Returns:

string with trouble info.

setArrayDesigns

public void setArrayDesigns(Collection<ArrayDesignValueObject> arrayDesigns)

As a side effect, sets the technology type and taxon of this based on the first arrayDesign.

Parameters:

arrayDesigns - arrayDesign value objects to associate