List<SequenceFeature> getAllFeatures(String... type);
/**
+ * Answers a list of all positional (or non-positional) features which are in
+ * the specified feature group, optionally restricted to features of specified
+ * types.
+ *
+ * @param positional
+ * if true returns positional features, else non-positional features
+ * @param group
+ * the feature group to be matched (which may be null)
+ * @param type
+ * optional feature types to filter by
+ * @return
+ */
+ List<SequenceFeature> getFeaturesForGroup(boolean positional,
+ String group, 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.
* @return
*/
float getMaximumScore(String type, boolean positional);
-}
\ No newline at end of file
+
+ /**
+ * Adds the shift amount to the start and end of all positional features whose
+ * start position is at or after fromPosition. Returns true if at least one
+ * feature was shifted, else false.
+ *
+ * @param fromPosition
+ * @param shiftBy
+ */
+ boolean shiftFeatures(int fromPosition, int shiftBy);
+
+ /**
+ * Deletes all positional and non-positional features
+ */
+ void deleteAll();
+}