Package ubic.gemma.model.expression.experiment

Class ExpressionExperimentDetailsValueObject

java.lang.Object
ubic.gemma.model.common.IdentifiableValueObject<ExpressionExperiment>
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:

  • Constructor Details

    • 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 Details

    • 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

      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

    • getArrayDesigns

      @Nullable public Collection<ArrayDesignValueObject> getArrayDesigns()

    • getDateArrayDesignLastUpdated

      public Date getDateArrayDesignLastUpdated()
      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 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()
      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()

    • getDifferentialExpressionAnalyses

      public Collection<DifferentialExpressionAnalysisValueObject> getDifferentialExpressionAnalyses()

    • getExpressionExperimentSets

      @Nullable public Collection<ExpressionExperimentSetValueObject> getExpressionExperimentSets()
      EE sets this experiment is part of.

    • getBatchFetchEventType

      public String getBatchFetchEventType()

    • getPcaAnalysisEventType

      public String getPcaAnalysisEventType()

    • getProcessedDataVectorComputationEventType

      public String getProcessedDataVectorComputationEventType()

    • getLastArrayDesignUpdateDate

      public String getLastArrayDesignUpdateDate()

    • getLinkAnalysisEventType

      public String getLinkAnalysisEventType()

    • getMissingValueAnalysisEventType

      public String getMissingValueAnalysisEventType()

    • getSampleRemovedFlags

      public Collection<AuditEventValueObject> getSampleRemovedFlags()
      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.

    • getNumAnnotations

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

    • getNumPopulatedFactors

      public Long getNumPopulatedFactors()
      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()
      Experiments that are related to this one via the splitting of a source experiment.

    • getPrimaryCitation

      public CitationValueObject getPrimaryCitation()

    • getPubmedId

      @Nullable public Integer getPubmedId()

    • getSecondaryAccession

      @Nullable public String getSecondaryAccession()
      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

      @Nullable public String getSecondaryExternalDatabase()

    • getSecondaryExternalUri

      @Nullable public String getSecondaryExternalUri()

    • getQChtml

      public String getQChtml()

    • getNumberOfCells

      @Nullable public Integer getNumberOfCells()
      The number of cells this experiment has.
      See Also:

    • getNumberOfCellIds

      public Integer getNumberOfCellIds()
      The number of cell IDs that the preferred single-cell dimension has.
      See Also:

    • isHasCellBrowser

      public boolean isHasCellBrowser()
      Indicate if this experiment has a Cell Browser associated with it.

    • getCellBrowserUrl

      @Nullable public String getCellBrowserUrl()
      URL for the Cell Browser, if available.

    • getCellBrowserDatasetName

      public String getCellBrowserDatasetName()

    • getFont

      @Nullable public String getFont()
      Font to use when rendering diagnostic plots, etc.

    • setDateArrayDesignLastUpdated

      public void setDateArrayDesignLastUpdated(Date dateArrayDesignLastUpdated)
      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 them. This is used to help flag experiments that need re-analysis due to changes in the underlying array design(s).

    • setDateBatchFetch

      public void setDateBatchFetch(Date dateBatchFetch)

    • setDateCached

      public void setDateCached(Date dateCached)
      The date this object was generated.

    • 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)

    • setDifferentialExpressionAnalyses

      public void setDifferentialExpressionAnalyses(Collection<DifferentialExpressionAnalysisValueObject> differentialExpressionAnalyses)

    • setExpressionExperimentSets

      public void setExpressionExperimentSets(@Nullable Collection<ExpressionExperimentSetValueObject> expressionExperimentSets)
      EE sets this experiment is part of.

    • setHasBatchInformation

      public void setHasBatchInformation(boolean hasBatchInformation)
      FIXME: rename this to hasUsableBatchInformation

    • setHasBothIntensities

      public void setHasBothIntensities(boolean hasBothIntensities)

    • setHasCoexpressionAnalysis

      public void setHasCoexpressionAnalysis(boolean hasCoexpressionAnalysis)

    • setHasDifferentialExpressionAnalysis

      public void setHasDifferentialExpressionAnalysis(boolean hasDifferentialExpressionAnalysis)

    • setHasEitherIntensity

      public void setHasEitherIntensity(boolean hasEitherIntensity)
      Indicate if the experiment has any intensity information available. Relevant for two-channel studies.

    • setHasMultiplePreferredQuantitationTypes

      public void setHasMultiplePreferredQuantitationTypes(boolean hasMultiplePreferredQuantitationTypes)

    • setHasMultipleTechnologyTypes

      public void setHasMultipleTechnologyTypes(boolean hasMultipleTechnologyTypes)

    • setReprocessedFromRawData

      public void setReprocessedFromRawData(boolean isReprocessedFromRawData)

    • setBatchFetchEventType

      public void setBatchFetchEventType(String batchFetchEventType)

    • setPcaAnalysisEventType

      public void setPcaAnalysisEventType(String pcaAnalysisEventType)

    • setProcessedDataVectorComputationEventType

      public void setProcessedDataVectorComputationEventType(String processedDataVectorComputationEventType)

    • setLastArrayDesignUpdateDate

      public void setLastArrayDesignUpdateDate(String lastArrayDesignUpdateDate)

    • setLinkAnalysisEventType

      public void setLinkAnalysisEventType(String linkAnalysisEventType)

    • setMissingValueAnalysisEventType

      public void setMissingValueAnalysisEventType(String missingValueAnalysisEventType)

    • setSampleRemovedFlags

      public void setSampleRemovedFlags(Collection<AuditEventValueObject> sampleRemovedFlags)
      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.

    • setNumAnnotations

      public void setNumAnnotations(Long numAnnotations)
      The number of terms (Characteristics) the experiment has to describe it.

    • setNumPopulatedFactors

      public void setNumPopulatedFactors(Long numPopulatedFactors)
      The number of experimental factors the experiment has (counting those that are populated with biomaterials).

    • setOriginalPlatforms

      public void setOriginalPlatforms(Collection<ArrayDesignValueObject> originalPlatforms)

    • setOtherParts

      public void setOtherParts(Collection<ExpressionExperimentValueObject> otherParts)
      Experiments that are related to this one via the splitting of a source experiment.

    • setPrimaryCitation

      public void setPrimaryCitation(CitationValueObject primaryCitation)

    • setPubmedId

      public void setPubmedId(@Nullable Integer pubmedId)

    • setSecondaryAccession

      public void setSecondaryAccession(@Nullable String secondaryAccession)
      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.

    • setSecondaryExternalDatabase

      public void setSecondaryExternalDatabase(@Nullable String secondaryExternalDatabase)

    • setSecondaryExternalUri

      public void setSecondaryExternalUri(@Nullable String secondaryExternalUri)

    • setQChtml

      public void setQChtml(String QChtml)

    • setNumberOfCells

      public void setNumberOfCells(@Nullable Integer numberOfCells)
      The number of cells this experiment has.
      See Also:

    • setNumberOfCellIds

      public void setNumberOfCellIds(Integer numberOfCellIds)
      The number of cell IDs that the preferred single-cell dimension has.
      See Also:

    • setHasCellBrowser

      public void setHasCellBrowser(boolean hasCellBrowser)
      Indicate if this experiment has a Cell Browser associated with it.

    • setCellBrowserUrl

      public void setCellBrowserUrl(@Nullable String cellBrowserUrl)
      URL for the Cell Browser, if available.

    • setCellBrowserDatasetName

      public void setCellBrowserDatasetName(String cellBrowserDatasetName)

    • setFont

      public void setFont(@Nullable String font)
      Font to use when rendering diagnostic plots, etc.