ubic.gemma.model.expression.experiment

Class ExpressionExperimentDetailsValueObject

java.lang.Object

ubic.gemma.model.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, Identifiable

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.IdentifiableValueObject

id

Constructor Summary

Constructors

Constructor and 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 and Description
void	auditEvents2SampleRemovedFlags(Collection<AuditEvent> s)
Boolean	getActuallyTroubled()
Collection<ArrayDesignValueObject>	getArrayDesigns()
String	getBatchFetchEventType()
Date	getDateArrayDesignLastUpdated()
Date	getDateBatchFetch()
Date	getDateCached()
Date	getDateDifferentialAnalysis()
Date	getDateLinkAnalysis()
Date	getDateMissingValueAnalysis()
Date	getDatePcaAnalysis()
Date	getDateProcessedDataVectorComputation()
String	getDescription()
Collection<DifferentialExpressionAnalysisValueObject>	getDifferentialExpressionAnalyses()
Collection<ExpressionExperimentSetValueObject>	getExpressionExperimentSets()
Boolean	getHasBothIntensities()
Boolean	getHasCoexpressionAnalysis()
Boolean	getHasDifferentialExpressionAnalysis()
Boolean	getHasEitherIntensity()
Boolean	getHasMultiplePreferredQuantitationTypes()
Boolean	getHasMultipleTechnologyTypes()
Boolean	getIsRNASeq()
String	getLastArrayDesignUpdateDate()
String	getLinkAnalysisEventType()
Double	getMinPvalue()
String	getMissingValueAnalysisEventType()
Integer	getNumAnnotations()
Integer	getNumPopulatedFactors()
Collection<ArrayDesignValueObject>	getOriginalPlatforms()
Collection<ExpressionExperimentValueObject>	getOtherParts()
String	getPcaAnalysisEventType()
Boolean	getPlatformTroubled()
CitationValueObject	getPrimaryCitation()
String	getProcessedDataVectorComputationEventType()
Integer	getPubmedId()
String	getQChtml()
boolean	getReprocessedFromRawData()
Collection<AuditEventValueObject>	getSampleRemovedFlags()
String	getSecondaryAccession()
String	getSecondaryExternalDatabase()
String	getSecondaryExternalUri()
Boolean	getTroubled()
String	getTroubleDetails()
String	getTroubleDetails(boolean htmlEscape) Checks trouble of this EE and all its Array Designs and returns compilation of trouble info.
boolean	isHasBatchInformation()
void	setArrayDesigns(Collection<ArrayDesignValueObject> arrayDesigns) As a side effect, sets the technology type and taxon of this based on the first arrayDesign.
void	setBatchFetchEventType(String batchFetchEventType)
void	setDateArrayDesignLastUpdated(Date dateArrayDesignLastUpdated)
void	setDateBatchFetch(Date dateBatchFetch)
void	setDateCached(Date dateCached)
void	setDateDifferentialAnalysis(Date dateDifferentialAnalysis)
void	setDateLinkAnalysis(Date dateLinkAnalysis)
void	setDateMissingValueAnalysis(Date dateMissingValueAnalysis)
void	setDatePcaAnalysis(Date datePcaAnalysis)
void	setDateProcessedDataVectorComputation(Date dateProcessedDataVectorComputation)
void	setDescription(String description)
void	setDifferentialExpressionAnalyses(Collection<DifferentialExpressionAnalysisValueObject> differentialExpressionAnalyses)
void	setExpressionExperimentSets(Collection<ExpressionExperimentSetValueObject> expressionExperimentSets)
void	setHasBatchInformation(boolean hasBatchInformation)
void	setHasBothIntensities(boolean hasBothIntensities)
void	setHasCoexpressionAnalysis(Boolean hasCoexpressionAnalysis)
void	setHasDifferentialExpressionAnalysis(Boolean hasDifferentialExpressionAnalysis)
void	setHasEitherIntensity(Boolean hasEitherIntensity)
void	setHasMultiplePreferredQuantitationTypes(Boolean hasMultiplePreferredQuantitationTypes)
void	setHasMultipleTechnologyTypes(Boolean hasMultipleTechnologyTypes)
void	setIsRNASeq(Boolean isRNASeq)
void	setLastArrayDesignUpdateDate(String lastArrayDesignUpdateDate)
void	setLinkAnalysisEventType(String linkAnalysisEventType)
void	setMinPvalue(Double minPvalue)
void	setMissingValueAnalysisEventType(String missingValueAnalysisEventType)
void	setNumAnnotations(Integer numAnnotations)
void	setNumPopulatedFactors(Integer numPopulatedFactors)
void	setOriginalPlatforms(Collection<ArrayDesignValueObject> originalPlatforms)
void	setPcaAnalysisEventType(String pcaAnalysisEventType)
void	setPrimaryCitation(CitationValueObject primaryCitation)
void	setProcessedDataVectorComputationEventType(String processedDataVectorComputationEventType)
void	setPubmedId(Integer pubmedId)
void	setQChtml(String qChtml)
void	setReprocessedFromRawData(boolean reprocessedFromRawData)
void	setSampleRemovedFlags(Collection<AuditEventValueObject> sampleRemovedFlags)
void	setSecondaryAccession(String secondaryAccession)
void	setSecondaryExternalDatabase(String secondaryExternalDatabase)
void	setSecondaryExternalUri(String secondaryExternalUri)

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

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

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

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

Methods inherited from class ubic.gemma.model.IdentifiableValueObject

getId, setId

Methods inherited from class java.lang.Object

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

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

auditEvents2SampleRemovedFlags

public void auditEvents2SampleRemovedFlags(Collection<AuditEvent> s)

getActuallyTroubled

public Boolean getActuallyTroubled()

Returns:

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

getArrayDesigns

public Collection<ArrayDesignValueObject> getArrayDesigns()

getBatchFetchEventType

public String getBatchFetchEventType()

getDateArrayDesignLastUpdated

public Date getDateArrayDesignLastUpdated()

Returns:

The date the platform associated with the experiment was last updated. If there are multiple platforms this should be the date of the most recent modification of any of them. This is used to help flag experiments that need re-analysis due to changes in the underlying array design(s)

getDateBatchFetch

public Date getDateBatchFetch()

getDateCached

public Date getDateCached()

Returns:

The date this object was generated.

getDateDifferentialAnalysis

public Date getDateDifferentialAnalysis()

getDateLinkAnalysis

public Date getDateLinkAnalysis()

getDateMissingValueAnalysis

public Date getDateMissingValueAnalysis()

getDatePcaAnalysis

public Date getDatePcaAnalysis()

getDateProcessedDataVectorComputation

public Date getDateProcessedDataVectorComputation()

getDescription

public String getDescription()

getDifferentialExpressionAnalyses

public Collection<DifferentialExpressionAnalysisValueObject> getDifferentialExpressionAnalyses()

getExpressionExperimentSets

public Collection<ExpressionExperimentSetValueObject> getExpressionExperimentSets()

Returns:

the expressionExperimentSets

getHasBothIntensities

public Boolean getHasBothIntensities()

getHasCoexpressionAnalysis

public Boolean getHasCoexpressionAnalysis()

getHasDifferentialExpressionAnalysis

public Boolean getHasDifferentialExpressionAnalysis()

getHasEitherIntensity

public Boolean getHasEitherIntensity()

Returns:

true if the experiment has any intensity information available. Relevant for two-channel studies.

getHasMultiplePreferredQuantitationTypes

public Boolean getHasMultiplePreferredQuantitationTypes()

getHasMultipleTechnologyTypes

public Boolean getHasMultipleTechnologyTypes()

getIsRNASeq

public Boolean getIsRNASeq()

getLastArrayDesignUpdateDate

public String getLastArrayDesignUpdateDate()

getLinkAnalysisEventType

public String getLinkAnalysisEventType()

getMinPvalue

public Double getMinPvalue()

getMissingValueAnalysisEventType

public String getMissingValueAnalysisEventType()

getNumAnnotations

public Integer getNumAnnotations()

Returns:

The number of terms (Characteristics) the experiment has to describe it.

getNumPopulatedFactors

public Integer getNumPopulatedFactors()

Returns:

The number of experimental factors the experiment has (counting those that are populated with biomaterials)

getOriginalPlatforms

public Collection<ArrayDesignValueObject> getOriginalPlatforms()

getOtherParts

public Collection<ExpressionExperimentValueObject> getOtherParts()

Returns:

IDs of experiments that are related to this one via the splitting of a source experiment.

getPcaAnalysisEventType

public String getPcaAnalysisEventType()

getPlatformTroubled

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.

getPrimaryCitation

public CitationValueObject getPrimaryCitation()

getProcessedDataVectorComputationEventType

public String getProcessedDataVectorComputationEventType()

getPubmedId

public Integer getPubmedId()

getQChtml

public String getQChtml()

getReprocessedFromRawData

public boolean getReprocessedFromRawData()

getSampleRemovedFlags

public Collection<AuditEventValueObject> getSampleRemovedFlags()

Returns:

Details of samples that were removed (or marked as outliers). This can happen multiple times in the life of data set, so this is a collection of AuditEvents.

getSecondaryAccession

public String getSecondaryAccession()

Returns:

Identifier in a second database, if available. For example, if the data are in GEO and in ArrayExpress, this might be a link to the ArrayExpress version.

getSecondaryExternalDatabase

public String getSecondaryExternalDatabase()

getSecondaryExternalUri

public String getSecondaryExternalUri()

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.

isHasBatchInformation

public boolean isHasBatchInformation()

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

setBatchFetchEventType

public void setBatchFetchEventType(String batchFetchEventType)

setDateArrayDesignLastUpdated

public void setDateArrayDesignLastUpdated(Date dateArrayDesignLastUpdated)

setDateBatchFetch

public void setDateBatchFetch(Date dateBatchFetch)

setDateCached

public void setDateCached(Date dateCached)

setDateDifferentialAnalysis

public void setDateDifferentialAnalysis(Date dateDifferentialAnalysis)

setDateLinkAnalysis

public void setDateLinkAnalysis(Date dateLinkAnalysis)

setDateMissingValueAnalysis

public void setDateMissingValueAnalysis(Date dateMissingValueAnalysis)

setDatePcaAnalysis

public void setDatePcaAnalysis(Date datePcaAnalysis)

setDateProcessedDataVectorComputation

public void setDateProcessedDataVectorComputation(Date dateProcessedDataVectorComputation)

setDescription

public void setDescription(String description)

setDifferentialExpressionAnalyses

public void setDifferentialExpressionAnalyses(Collection<DifferentialExpressionAnalysisValueObject> differentialExpressionAnalyses)

setExpressionExperimentSets

public void setExpressionExperimentSets(Collection<ExpressionExperimentSetValueObject> expressionExperimentSets)

Parameters:

expressionExperimentSets - the expressionExperimentSets to set

setHasBatchInformation

public void setHasBatchInformation(boolean hasBatchInformation)

setHasBothIntensities

public void setHasBothIntensities(boolean hasBothIntensities)

setHasCoexpressionAnalysis

public void setHasCoexpressionAnalysis(Boolean hasCoexpressionAnalysis)

setHasDifferentialExpressionAnalysis

public void setHasDifferentialExpressionAnalysis(Boolean hasDifferentialExpressionAnalysis)

setHasEitherIntensity

public void setHasEitherIntensity(Boolean hasEitherIntensity)

setHasMultiplePreferredQuantitationTypes

public void setHasMultiplePreferredQuantitationTypes(Boolean hasMultiplePreferredQuantitationTypes)

setHasMultipleTechnologyTypes

public void setHasMultipleTechnologyTypes(Boolean hasMultipleTechnologyTypes)

setIsRNASeq

public void setIsRNASeq(Boolean isRNASeq)

setLastArrayDesignUpdateDate

public void setLastArrayDesignUpdateDate(String lastArrayDesignUpdateDate)

setLinkAnalysisEventType

public void setLinkAnalysisEventType(String linkAnalysisEventType)

setMinPvalue

public void setMinPvalue(Double minPvalue)

setMissingValueAnalysisEventType

public void setMissingValueAnalysisEventType(String missingValueAnalysisEventType)

setNumAnnotations

public void setNumAnnotations(Integer numAnnotations)

setNumPopulatedFactors

public void setNumPopulatedFactors(Integer numPopulatedFactors)

setOriginalPlatforms

public void setOriginalPlatforms(Collection<ArrayDesignValueObject> originalPlatforms)

setPcaAnalysisEventType

public void setPcaAnalysisEventType(String pcaAnalysisEventType)

setPrimaryCitation

public void setPrimaryCitation(CitationValueObject primaryCitation)

setProcessedDataVectorComputationEventType

public void setProcessedDataVectorComputationEventType(String processedDataVectorComputationEventType)

setPubmedId

public void setPubmedId(Integer pubmedId)

setQChtml

public void setQChtml(String qChtml)

setReprocessedFromRawData

public void setReprocessedFromRawData(boolean reprocessedFromRawData)

setSampleRemovedFlags

public void setSampleRemovedFlags(Collection<AuditEventValueObject> sampleRemovedFlags)

setSecondaryAccession

public void setSecondaryAccession(String secondaryAccession)

setSecondaryExternalDatabase

public void setSecondaryExternalDatabase(String secondaryExternalDatabase)

setSecondaryExternalUri

public void setSecondaryExternalUri(String secondaryExternalUri)