Package ubic.gemma.model.expression.experiment

Class FactorValue

java.lang.Object
ubic.gemma.model.common.AbstractIdentifiable
ubic.gemma.model.expression.experiment.FactorValue
All Implemented Interfaces:
gemma.gsec.model.Securable, gemma.gsec.model.SecuredChild, Securable, SecuredChild<ExpressionExperiment>, Identifiable
@Indexed public class FactorValue extends AbstractIdentifiable implements SecuredChild<ExpressionExperiment>
The value for a ExperimentalFactor, representing a specific instance of the factor, such as "10 ug/kg" or "mutant"

  • Constructor Details

    • FactorValue

      public FactorValue()

  • Method Details

    • 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

    • getExperimentalFactor

      public ExperimentalFactor getExperimentalFactor()

    • setExperimentalFactor

      public void setExperimentalFactor(ExperimentalFactor experimentalFactor)

    • getIsBaseline

      @Nullable public Boolean getIsBaseline()
      Indicate if this factor value is a "forced" baseline or non-baseline condition.

      This is ignored if the factor is continuous.

    • setIsBaseline

      public void setIsBaseline(@Nullable Boolean isBaseline)

    • getValue

      @Nullable @Deprecated public String getValue()
      Deprecated.
      use getMeasurement() or getCharacteristics() to retrieve the value.

    • setValue

      @Deprecated public void setValue(@Nullable String value)
      Deprecated.

    • getMeasurement

      @Nullable public Measurement getMeasurement()
      If this is a continuous factor, a measurement representing its value.

    • setMeasurement

      public void setMeasurement(@Nullable Measurement measurement)

    • getCharacteristics

      @IndexedEmbedded public Set<Statement> getCharacteristics()
      Collection of Statement describing this factor value.

    • setCharacteristics

      public void setCharacteristics(Set<Statement> characteristics)

    • getOldStyleCharacteristics

      @Deprecated public Set<Characteristic> getOldStyleCharacteristics()
      Deprecated.
      Old-style characteristics from the 1.30 series.

      This will be removed when all the characteristics are ported to the new style using Statement.

    • setOldStyleCharacteristics

      @Deprecated public void setOldStyleCharacteristics(Set<Characteristic> oldCharacteristics)
      Deprecated.

    • getNeedsAttention

      public boolean getNeedsAttention()
      Indicate if this factor value needs attention.

      If this is the case, there might be a FactorValueNeedsAttentionEvent event attached to the owning ExpressionExperiment with additional details.

    • setNeedsAttention

      public void setNeedsAttention(boolean troubled)

    • getSecurityOwner

      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(ExpressionExperiment ee)

    • hashCode

      public int hashCode()
      Description copied from class: AbstractIdentifiable
      Important note: Never use the ID in the hashCode() implementation since it can be assigned when the object is persisted.
      Specified by:
      hashCode in class AbstractIdentifiable

    • equals

      public boolean equals(Object object)
      Description copied from class: AbstractIdentifiable
      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 AbstractIdentifiable

    • toString

      public String toString()
      Overrides:
      toString in class AbstractIdentifiable