Package ubic.gemma.model.expression.bioAssay

Class BioAssay

java.lang.Object
ubic.gemma.model.common.AbstractIdentifiable
ubic.gemma.model.common.AbstractDescribable
ubic.gemma.model.expression.bioAssay.BioAssay
All Implemented Interfaces:
gemma.gsec.model.Securable, gemma.gsec.model.SecuredChild, Securable, SecuredChild<ExpressionExperiment>, Describable, Identifiable
@Indexed public class BioAssay extends AbstractDescribable implements SecuredChild<ExpressionExperiment>
Represents the bringing together of a biomaterial with an assay of some sort (typically an expression assay). We don't distinguish between "physical" and "computational" BioAssays, so this is a concrete class. This has several slots that are used specifically to support sequence-based data, but is intended to be generic.

  • Field Details

  • Constructor Details

    • BioAssay

      public BioAssay()

  • Method Details

    • hashCode

      public int hashCode()
      Description copied from class: AbstractDescribable
      The default hash code for a describable is based on its name, ignoring case.

      Important note: Never use the ID in the hashCode() implementation since it can be assigned when the object is persisted.

      Overrides:
      hashCode in class AbstractDescribable

    • equals

      public boolean equals(Object object)
      Description copied from class: AbstractDescribable
      Important note: The name should be compared in a case-insensitive manner. You can use DescribableUtils.equalsByName(Describable, Describable) to get the correct behavior.

      Important note: Two objects with the same class and non-null ID must be considered equal. If one or both IDs are nulls, the rest of the state can be used to determine equality.

      Specified by:
      equals in class AbstractDescribable

    • getId

      @DocumentId public Long getId()
      Description copied from interface: Identifiable
      Obtain the identifier of the object.
      Specified by:
      getId in interface Identifiable
      Specified by:
      getId in interface gemma.gsec.model.Securable
      Overrides:
      getId in class AbstractIdentifiable

    • getShortName

      @Nullable @Field public String getShortName()

    • setShortName

      public void setShortName(@Nullable String shortName)

    • getName

      @Field public String getName()
      Description copied from interface: Describable
      Obtain the name of the object.

      It may be human-readable.

      It is case-insensitive and usually unique within a certain context (e.g. in a collection).

      It is non-null by default, but implementation may override this with a Nullable annotation. If null, it should not be treated as equal to other Describable objects (i.e. there can be multiple null-named describable within a given set).

      Specified by:
      getName in interface Describable
      Overrides:
      getName in class AbstractDescribable

    • getDescription

      @Field(store=YES) public String getDescription()
      Description copied from interface: Describable
      Obtain a human-readable description of the object
      Specified by:
      getDescription in interface Describable
      Overrides:
      getDescription in class AbstractDescribable

    • getAccession

      @Nullable @IndexedEmbedded public DatabaseEntry getAccession()

    • setAccession

      public void setAccession(@Nullable DatabaseEntry accession)

    • getArrayDesignUsed

      public ArrayDesign getArrayDesignUsed()

    • setArrayDesignUsed

      public void setArrayDesignUsed(ArrayDesign arrayDesignUsed)

    • getIsOutlier

      public boolean getIsOutlier()

    • setIsOutlier

      public void setIsOutlier(boolean isOutlier)

    • getProcessingDate

      @Nullable public Date getProcessingDate()

    • setProcessingDate

      public void setProcessingDate(@Nullable Date processingDate)

    • getSampleUsed

      @IndexedEmbedded public BioMaterial getSampleUsed()

    • setSampleUsed

      public void setSampleUsed(BioMaterial sampleUsed)

    • getSecurityOwner

      @Nullable public ExpressionExperiment getSecurityOwner()
      Description copied from interface: SecuredChild
      Obtain the security owner of this secured child.

      Secured children should always have an owner in the ACL table, but that relation is not always direct or mapped. A more robust way of checking is to look up the parent via AclObjectIdentity.getParentObject(). If the security owner cannot be determined, the implementation should define a setter so it can be temporarily assigned for creating the ACL identity.

      Specified by:
      getSecurityOwner in interface gemma.gsec.model.SecuredChild
      Specified by:
      getSecurityOwner in interface SecuredChild<ExpressionExperiment>
      Returns:
      the security owner, or null if not known.

    • setSecurityOwner

      public void setSecurityOwner(@Nullable ExpressionExperiment securable)

    • getSequencePairedReads

      @Nullable public Boolean getSequencePairedReads()

    • setSequencePairedReads

      public void setSequencePairedReads(@Nullable Boolean sequencePairedReads)

    • getSequenceReadCount

      @Nullable public Long getSequenceReadCount()

    • setSequenceReadCount

      public void setSequenceReadCount(@Nullable Long sequenceReadCount)

    • getSequenceReadLength

      @Nullable public Integer getSequenceReadLength()

    • setSequenceReadLength

      public void setSequenceReadLength(@Nullable Integer sequenceReadLength)

    • getMetadata

      @Nullable public String getMetadata()

    • setMetadata

      public void setMetadata(@Nullable String metadata)

    • getOriginalPlatform

      @Nullable public ArrayDesign getOriginalPlatform()

    • setOriginalPlatform

      public void setOriginalPlatform(@Nullable ArrayDesign originalPlatform)

    • getFastqHeaders

      @Nullable public String getFastqHeaders()

    • setFastqHeaders

      public void setFastqHeaders(@Nullable String fastqHeaders)

    • getNumberOfCells

      @Nullable public Integer getNumberOfCells()

    • setNumberOfCells

      public void setNumberOfCells(@Nullable Integer numberOfCells)

    • getNumberOfDesignElements

      @Nullable public Integer getNumberOfDesignElements()

    • setNumberOfDesignElements

      public void setNumberOfDesignElements(@Nullable Integer numberOfDesignElements)

    • getNumberOfCellsByDesignElements

      @Nullable public Integer getNumberOfCellsByDesignElements()

    • setNumberOfCellsByDesignElements

      public void setNumberOfCellsByDesignElements(@Nullable Integer numberOfCellsByDesignElements)