List<SequenceFeature> getAllFeatures(String... type);
/**
+ * Answers a list of all features stored, whose type either matches one of the
+ * given ontology terms, or is a specialisation of a term in the Sequence
+ * Ontology. Results are returned in no particular guaranteed order.
+ *
+ * @param ontologyTerm
+ * @return
+ */
+ List<SequenceFeature> getFeaturesByOntology(String... ontologyTerm);
+
+ /**
* Answers the number of (positional or non-positional) features, optionally
* restricted to specified feature types. Contact features are counted as 1.
*
boolean positionalFeatures, String... groups);
/**
- * Answers a set of the distinct feature types for which a feature is stored
+ * Answers a set of the distinct feature types for which a feature is stored.
+ * The types may optionally be restricted to those which match, or are a
+ * subtype of, given sequence ontology terms
*
* @return
*/
- Set<String> getFeatureTypes();
+ Set<String> getFeatureTypes(String... soTerm);
/**
* Answers the minimum score held for positional or non-positional features