Class AnnotationValueObject

java.lang.Object
ubic.gemma.model.common.IdentifiableValueObject<Characteristic>
ubic.gemma.model.common.description.AnnotationValueObject
All Implemented Interfaces:
Serializable, Identifiable
Direct Known Subclasses:
DatasetsWebService.AnnotationWithUsageStatisticsValueObject
public class AnnotationValueObject extends IdentifiableValueObject<Characteristic>
Author:
luke
See Also:

  • Constructor Details

    • AnnotationValueObject

      public AnnotationValueObject()

    • AnnotationValueObject

      public AnnotationValueObject(Long id)

    • AnnotationValueObject

      public AnnotationValueObject(String categoryUri, String category, String valueUri, String value, Class<?> objectClass)

    • AnnotationValueObject

      public AnnotationValueObject(Characteristic c)

    • AnnotationValueObject

      public AnnotationValueObject(Characteristic c, Class<?> objectClass)

  • Method Details

    • toString

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

    • getCategoryUri

      public String getCategoryUri()
      Category URI. Same field as Characteristic.getCategoryUri(), under the same name.

    • getCategory

      public String getCategory()
      Category label. Same field as Characteristic.getCategory(), under the same name.

    • getValueUri

      public String getValueUri()
      URI of the annotated term. On a Statement row this is the subject's URI.

    • getValue

      public String getValue()
      Label of the annotated term — the value as curated. On a Statement row this is the subject's label, and the predicate / object labels stay in their own fields: this field never carries a composed sentence. FactorValueUtils.getSummaryString(FactorValue) is the separate sentence-builder for display.

    • getDescription

      public String getDescription()

    • getEvidenceCode

      public String getEvidenceCode()

    • getObjectClass

      public String getObjectClass()

    • getPredicate

      @Nullable public String getPredicate()
      Predicate label for Statement-backed annotations (e.g. "has_dose"). Null when the underlying row is a plain Characteristic. The predicate* / object* pair, together with the optional secondPredicate* / secondObject* pair, exposes the Statement relational shape to read-side consumers without breaking the Characteristic wire shape — valueUri and value carry the statement's subject URI and label (Statement aliases subject → value internally).

    • getPredicateUri

      @Nullable public String getPredicateUri()

    • getObject

      @Nullable public String getObject()

    • getObjectUri

      @Nullable public String getObjectUri()

    • getSecondPredicate

      @Nullable public String getSecondPredicate()

    • getSecondPredicateUri

      @Nullable public String getSecondPredicateUri()

    • getSecondObject

      @Nullable public String getSecondObject()

    • getSecondObjectUri

      @Nullable public String getSecondObjectUri()

    • getParentName

      public String getParentName()

    • getParentDescription

      public String getParentDescription()

    • getParentLink

      public String getParentLink()

    • getParentOfParentName

      public String getParentOfParentName()

    • getParentOfParentDescription

      public String getParentOfParentDescription()

    • getParentOfParentLink

      public String getParentOfParentLink()

    • getSupportingEvidence

      @Nullable public com.fasterxml.jackson.databind.JsonNode getSupportingEvidence()
      Verbatim provenance backing a curated tag — a JSON array of {quote, source, location, ...} items the curation agents emitted (the agents-side FindingEvidence shape). Gemma stores and serves it opaquely, so the agents repo owns the schema. Null when the tag has no recorded evidence (plain/legacy tags, and ontology-term hits that were never accepted from a proposal).

    • setCategoryUri

      public void setCategoryUri(String categoryUri)
      Category URI. Same field as Characteristic.getCategoryUri(), under the same name.

    • setCategory

      public void setCategory(String category)
      Category label. Same field as Characteristic.getCategory(), under the same name.

    • setValueUri

      public void setValueUri(String valueUri)
      URI of the annotated term. On a Statement row this is the subject's URI.

    • setValue

      public void setValue(String value)
      Label of the annotated term — the value as curated. On a Statement row this is the subject's label, and the predicate / object labels stay in their own fields: this field never carries a composed sentence. FactorValueUtils.getSummaryString(FactorValue) is the separate sentence-builder for display.

    • setDescription

      public void setDescription(String description)

    • setEvidenceCode

      public void setEvidenceCode(String evidenceCode)

    • setObjectClass

      public void setObjectClass(String objectClass)

    • setPredicate

      public void setPredicate(@Nullable String predicate)
      Predicate label for Statement-backed annotations (e.g. "has_dose"). Null when the underlying row is a plain Characteristic. The predicate* / object* pair, together with the optional secondPredicate* / secondObject* pair, exposes the Statement relational shape to read-side consumers without breaking the Characteristic wire shape — valueUri and value carry the statement's subject URI and label (Statement aliases subject → value internally).

    • setPredicateUri

      public void setPredicateUri(@Nullable String predicateUri)

    • setObject

      public void setObject(@Nullable String object)

    • setObjectUri

      public void setObjectUri(@Nullable String objectUri)

    • setSecondPredicate

      public void setSecondPredicate(@Nullable String secondPredicate)

    • setSecondPredicateUri

      public void setSecondPredicateUri(@Nullable String secondPredicateUri)

    • setSecondObject

      public void setSecondObject(@Nullable String secondObject)

    • setSecondObjectUri

      public void setSecondObjectUri(@Nullable String secondObjectUri)

    • setParentName

      public void setParentName(String parentName)

    • setParentDescription

      public void setParentDescription(String parentDescription)

    • setParentLink

      public void setParentLink(String parentLink)

    • setParentOfParentName

      public void setParentOfParentName(String parentOfParentName)

    • setParentOfParentDescription

      public void setParentOfParentDescription(String parentOfParentDescription)

    • setParentOfParentLink

      public void setParentOfParentLink(String parentOfParentLink)

    • setSupportingEvidence

      public void setSupportingEvidence(@Nullable com.fasterxml.jackson.databind.JsonNode supportingEvidence)
      Verbatim provenance backing a curated tag — a JSON array of {quote, source, location, ...} items the curation agents emitted (the agents-side FindingEvidence shape). Gemma stores and serves it opaquely, so the agents repo owns the schema. Null when the tag has no recorded evidence (plain/legacy tags, and ontology-term hits that were never accepted from a proposal).

    • equals

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

    • canEqual

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

    • hashCode

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