diff --git a/phenol-core/src/main/java/org/monarchinitiative/phenol/ontology/data/TermAnnotation.java b/phenol-core/src/main/java/org/monarchinitiative/phenol/ontology/data/TermAnnotation.java index a67076457..87f07285e 100644 --- a/phenol-core/src/main/java/org/monarchinitiative/phenol/ontology/data/TermAnnotation.java +++ b/phenol-core/src/main/java/org/monarchinitiative/phenol/ontology/data/TermAnnotation.java @@ -4,16 +4,12 @@ import java.util.Optional; /** - * A {@link TermAnnotation} links a {@link TermId} to a String label of a "world - * object". - * - *

For all annotated "world objects", the labels have to be unique for each object. The + * A {@link TermAnnotation} links a {@link TermId} to {@link TermId} of a "world object". + *

+ * For all annotated "world objects", the labels have to be unique for each object. The * annotations can then be used for, e.g., feeding into the information content computation and thus * into the similarity metrics computation algorithms. * - *

Implementing classes have to properly implement hashValue() and equals() - * . - * * @author Manuel Holtgrewe * @author Sebastian Koehler */ @@ -21,27 +17,22 @@ public interface TermAnnotation extends Identified, Serializable, Comparable + * Note, this is NOT the annotation ID which can be obtained by {@link #id()}. */ TermId getItemId(); /** - * Query for evidence code. - * - *

The default implementation returns an empty {@link Optional} value. - * - * @return Optional {@code String} with the identifier of the evidence code. + * Get an optional with an evidence code of the annotation. */ + // TODO - should we really return EvidenceCode here? default Optional getEvidenceCode() { return Optional.empty(); } /** - * Query for frequency of annotation in percent. - * - *

The default implementation always returns {@code Optional.empty()}. + * Get an optional frequency of the annotation in percent. */ default Optional getFrequency() { return Optional.empty();