Package ubic.gemma.model.expression.experiment

Class ExpressionExperimentDetailsValueObject

    • 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)

    • 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.

      • 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()

      • 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 Long getNumAnnotations()
        Returns:
        The number of terms (Characteristics) the experiment has to describe it.

      • getNumPopulatedFactors

        public Long getNumPopulatedFactors()
        Returns:
        The number of experimental factors the experiment has (counting those that are populated with biomaterials)

      • 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.

      • 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()

      • 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)

      • 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​(Long numAnnotations)

      • setNumPopulatedFactors

        public void setNumPopulatedFactors​(Long numPopulatedFactors)

      • setPcaAnalysisEventType

        public void setPcaAnalysisEventType​(String pcaAnalysisEventType)

      • setProcessedDataVectorComputationEventType

        public void setProcessedDataVectorComputationEventType​(String processedDataVectorComputationEventType)

      • setPubmedId

        public void setPubmedId​(Integer pubmedId)

      • setQChtml

        public void setQChtml​(String qChtml)

      • setReprocessedFromRawData

        public void setReprocessedFromRawData​(boolean reprocessedFromRawData)

      • setSecondaryAccession

        public void setSecondaryAccession​(String secondaryAccession)

      • setSecondaryExternalDatabase

        public void setSecondaryExternalDatabase​(String secondaryExternalDatabase)

      • setSecondaryExternalUri

        public void setSecondaryExternalUri​(String secondaryExternalUri)