Class AbstractFactorValueValueObject

java.lang.Object
ubic.gemma.model.common.IdentifiableValueObject<FactorValue>
ubic.gemma.model.expression.experiment.AbstractFactorValueValueObject
All Implemented Interfaces:
Serializable, Identifiable
Direct Known Subclasses:
FactorValueBasicValueObject, FactorValueValueObject
public abstract class AbstractFactorValueValueObject extends IdentifiableValueObject<FactorValue>
The bare minimum to represent a factor value.

This class solely exist to get consistent behavior between the deprecated FactorValueValueObject and its replacement FactorValueBasicValueObject.

Author:
poirigui
See Also:

  • Constructor Details

    • AbstractFactorValueValueObject

      protected AbstractFactorValueValueObject()

    • AbstractFactorValueValueObject

      protected AbstractFactorValueValueObject(Long id)

    • AbstractFactorValueValueObject

      protected AbstractFactorValueValueObject(FactorValue fv, boolean includeExperimentalFactor)

  • Method Details

    • isMeasurement

      public boolean isMeasurement()
      Indicate if this FactorValue is a measurement.

    • getOntologyId

      public String getOntologyId()
      A unique ontology identifier (i.e. IRI) for this factor value.

    • getExperimentalFactorId

      public Long getExperimentalFactorId()
      The ID of the experimental factor this factor value belongs to.

    • getExperimentalFactorType

      public String getExperimentalFactorType()
      The experimental factor type.

    • getExperimentalFactorCategory

      public CharacteristicValueObject getExperimentalFactorCategory()
      The experiment factor category.

    • getMeasurementObject

      public MeasurementValueObject getMeasurementObject()
      The measurement associated with this factor value.

      This is named as such to avoid conflict with isMeasurement().

    • getCharacteristics

      public List<CharacteristicValueObject> getCharacteristics()
      The characteristics associated with this factor value.

    • getStatements

      public List<StatementValueObject> getStatements()
      The statements associated with this factor value.

    • getBaseline

      public Boolean getBaseline()
      Whether this factor value is a "forced" baseline condition. Mirrors FactorValue.getIsBaseline(); null when unset. Ignored for continuous factors. Exposed on the wire as isBaseline so the design read/write round-trip (e.g. the composite curation commit) can carry the baseline flag.

    • getSupportingEvidence

      @Nullable public com.fasterxml.jackson.databind.JsonNode getSupportingEvidence()
      Verbatim provenance backing this factor VALUE — a JSON array of {quote, source, location, …} items the curation agents emitted. Gemma stores and serves it opaquely; the agents repo owns the schema.

      🛑 Not a roll-up of the evidence on statements, and not a fallback for it. A statement's evidence backs its triple; this backs the value — its label, its baseline flag, its measurement, the samples it covers — and a value carrying no statements at all still has a curator behind those choices. Reading one for the other conflates two levels that a composed factor value keeps apart.

      Null means nothing was recorded, which is the expected reading for most rows.

    • getSummary

      public String getSummary()
      Human-readable summary of the factor value.

    • setOntologyId

      public void setOntologyId(String ontologyId)
      A unique ontology identifier (i.e. IRI) for this factor value.

    • setExperimentalFactorId

      public void setExperimentalFactorId(Long experimentalFactorId)
      The ID of the experimental factor this factor value belongs to.

    • setExperimentalFactorType

      public void setExperimentalFactorType(String experimentalFactorType)
      The experimental factor type.

    • setExperimentalFactorCategory

      public void setExperimentalFactorCategory(CharacteristicValueObject experimentalFactorCategory)
      The experiment factor category.

    • setMeasurementObject

      public void setMeasurementObject(MeasurementValueObject measurementObject)
      The measurement associated with this factor value.

      This is named as such to avoid conflict with isMeasurement().

    • setCharacteristics

      public void setCharacteristics(List<CharacteristicValueObject> characteristics)
      The characteristics associated with this factor value.

    • setStatements

      public void setStatements(List<StatementValueObject> statements)
      The statements associated with this factor value.

    • setBaseline

      public void setBaseline(Boolean baseline)
      Whether this factor value is a "forced" baseline condition. Mirrors FactorValue.getIsBaseline(); null when unset. Ignored for continuous factors. Exposed on the wire as isBaseline so the design read/write round-trip (e.g. the composite curation commit) can carry the baseline flag.

    • setSupportingEvidence

      public void setSupportingEvidence(@Nullable com.fasterxml.jackson.databind.JsonNode supportingEvidence)
      Verbatim provenance backing this factor VALUE — a JSON array of {quote, source, location, …} items the curation agents emitted. Gemma stores and serves it opaquely; the agents repo owns the schema.

      🛑 Not a roll-up of the evidence on statements, and not a fallback for it. A statement's evidence backs its triple; this backs the value — its label, its baseline flag, its measurement, the samples it covers — and a value carrying no statements at all still has a curator behind those choices. Reading one for the other conflates two levels that a composed factor value keeps apart.

      Null means nothing was recorded, which is the expected reading for most rows.

    • setSummary

      public void setSummary(String summary)
      Human-readable summary of the factor value.

    • equals

      public boolean equals(Object o)
      Overrides:
      equals in class IdentifiableValueObject<FactorValue>

    • canEqual

      protected boolean canEqual(Object other)
      Overrides:
      canEqual in class IdentifiableValueObject<FactorValue>

    • hashCode

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