Package ubic.gemma.model.expression.bioAssay

Class BioAssayValueObject

java.lang.Object
ubic.gemma.model.common.IdentifiableValueObject<BioAssay>
ubic.gemma.model.expression.bioAssay.BioAssayValueObject
All Implemented Interfaces:
Serializable, Identifiable
public class BioAssayValueObject extends IdentifiableValueObject<BioAssay>
Author:
Paul
See Also:

  • Constructor Details

    • BioAssayValueObject

      public BioAssayValueObject()
      Required when using the class as a spring bean.

    • BioAssayValueObject

      public BioAssayValueObject(BioAssay bioAssay)

    • BioAssayValueObject

      public BioAssayValueObject(BioAssay bioAssay, boolean basic)

    • BioAssayValueObject

      public BioAssayValueObject(BioAssay bioAssay, boolean basic, boolean predictedOutlier)

    • BioAssayValueObject

      public BioAssayValueObject(BioAssay bioAssay, @Nullable Map<ArrayDesign,ArrayDesignValueObject> ad2vo, @Nullable BioAssay sourceBioAssay, boolean basic, boolean allFactorValues)
      Parameters:
      ad2vo - pre-populated array design VOs by array design, or null to ignore and the VOs will be initialized via ArrayDesignValueObject(ArrayDesign)
      sourceBioAssay - the source BioAssay if known, this corresponds to the assay of the source sample, but since there might be more than one, it must be picked explicitly based on the context
      basic - if true, produce basic factor values in the corresponding biomaterial, see BioMaterialValueObject(BioMaterial, boolean, boolean) for more details
      allFactorValues - include all FVs, including those inherited from the source biomaterial in the corresponding biomaterial

    • BioAssayValueObject

      public BioAssayValueObject(Long id)

  • Method Details

    • equals

      public boolean equals(Object obj)
      Overrides:
      equals in class IdentifiableValueObject<BioAssay>

    • hashCode

      public int hashCode()
      Overrides:
      hashCode in class IdentifiableValueObject<BioAssay>

    • toString

      public String toString()
      Overrides:
      toString in class IdentifiableValueObject<BioAssay>

    • getShortName

      @Nullable public String getShortName()

    • getName

      public String getName()

    • getDescription

      public String getDescription()

    • getMetadata

      public String getMetadata()

    • getAccession

      @Nullable public DatabaseEntryValueObject getAccession()

    • getArrayDesign

      public ArrayDesignValueObject getArrayDesign()

    • getOriginalPlatform

      @Nullable public ArrayDesignValueObject getOriginalPlatform()

    • getProcessingDate

      public Date getProcessingDate()

    • getSample

      public BioMaterialValueObject getSample()

    • getSequencePairedReads

      public Boolean getSequencePairedReads()

    • getSequenceReadCount

      public Long getSequenceReadCount()

    • getSequenceReadLength

      public Integer getSequenceReadLength()

    • isOutlier

      public boolean isOutlier()

    • isPredictedOutlier

      public boolean isPredictedOutlier()

    • isUserFlaggedOutlier

      public boolean isUserFlaggedOutlier()

    • getSourceBioAssayId

      @Nullable public Long getSourceBioAssayId()
      If this BioAssay has a parent via BioMaterial.getSourceBioMaterial(), this is the ID.

      This is context-dependent because the parent depends on which BioAssaySet is under consideration. For example, an experiment could have two sets of EE subsets with distinct parents.

    • setShortName

      public void setShortName(@Nullable String shortName)

    • setName

      public void setName(String name)

    • setDescription

      public void setDescription(String description)

    • setMetadata

      public void setMetadata(String metadata)

    • setAccession

      public void setAccession(@Nullable DatabaseEntryValueObject accession)

    • setArrayDesign

      public void setArrayDesign(ArrayDesignValueObject arrayDesign)

    • setOriginalPlatform

      public void setOriginalPlatform(@Nullable ArrayDesignValueObject originalPlatform)

    • setProcessingDate

      public void setProcessingDate(Date processingDate)

    • setSample

      public void setSample(BioMaterialValueObject sample)

    • setSequencePairedReads

      public void setSequencePairedReads(Boolean sequencePairedReads)

    • setSequenceReadCount

      public void setSequenceReadCount(Long sequenceReadCount)

    • setSequenceReadLength

      public void setSequenceReadLength(Integer sequenceReadLength)

    • setOutlier

      public void setOutlier(boolean outlier)

    • setPredictedOutlier

      public void setPredictedOutlier(boolean predictedOutlier)

    • setUserFlaggedOutlier

      public void setUserFlaggedOutlier(boolean userFlaggedOutlier)

    • setSourceBioAssayId

      public void setSourceBioAssayId(@Nullable Long sourceBioAssayId)
      If this BioAssay has a parent via BioMaterial.getSourceBioMaterial(), this is the ID.

      This is context-dependent because the parent depends on which BioAssaySet is under consideration. For example, an experiment could have two sets of EE subsets with distinct parents.