findFeatures(int from, int to, String... type);
/**
* Answers a list of all features stored, in no particular guaranteed order.
* Positional features may optionally be restricted to specified types, but
* all non-positional features (if any) are always returned.
*
* To filter non-positional features by type, use
* getNonPositionalFeatures(type).
*
* @param type
* @return
*/
List 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 getFeaturesForGroup(boolean positional,
String group, String... type);
/**
* Answers a list of all features stored, whose type either matches, or is a
* specialisation (in the Sequence Ontology) of, one of the given terms.
* Results are returned in no particular order.
*
* @param ontologyTerm
* @return
*/
List getFeaturesByOntology(String... ontologyTerm);
/**
* Answers the number of (positional or non-positional) features, optionally
* restricted to specified feature types. Contact features are counted as 1.
*
* @param positional
* @param type
* @return
*/
int getFeatureCount(boolean positional, String... type);
/**
* Answers the total length of positional features, optionally restricted to
* specified feature types. Contact features are counted as length 1.
*
* @param type
* @return
*/
int getTotalFeatureLength(String... type);
/**
* Answers a list of all positional features, optionally restricted to
* specified types, in no particular guaranteed order
*
* @param type
* @return
*/
List getPositionalFeatures(String... type);
/**
* Answers a list of all contact features, optionally restricted to specified
* types, in no particular guaranteed order
*
* @return
*/
List getContactFeatures(String... type);
/**
* Answers a list of all non-positional features, optionally restricted to
* specified types, in no particular guaranteed order
*
* @param type
* if no type is specified, all are returned
* @return
*/
List getNonPositionalFeatures(String... type);
/**
* Deletes the given feature from the store, returning true if it was found
* (and deleted), else false. This method makes no assumption that the feature
* is in the 'expected' place in the store, in case it has been modified since
* it was added.
*
* @param sf
*/
boolean delete(SequenceFeature sf);
/**
* Answers true if this store contains at least one feature, else false
*
* @return
*/
boolean hasFeatures();
/**
* Returns a set of the distinct feature groups present in the collection. The
* set may include null. The boolean parameter determines whether the groups
* for positional or for non-positional features are returned. The optional
* type parameter may be used to restrict to groups for specified feature
* types.
*
* @param positionalFeatures
* @param type
* @return
*/
Set getFeatureGroups(boolean positionalFeatures, String... type);
/**
* Answers the set of distinct feature types for which there is at least one
* feature with one of the given feature group(s). The boolean parameter
* determines whether the groups for positional or for non-positional features
* are returned.
*
* @param positionalFeatures
* @param groups
* @return
*/
Set getFeatureTypesForGroups(boolean positionalFeatures,
String... groups);
/**
* 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 getFeatureTypes(String... soTerm);
/**
* Answers the minimum score held for positional or non-positional features
* for the specified type. This may be Float.NaN if there are no features, or
* none has a non-NaN score.
*
* @param type
* @param positional
* @return
*/
float getMinimumScore(String type, boolean positional);
/**
* Answers the maximum score held for positional or non-positional features
* for the specified type. This may be Float.NaN if there are no features, or
* none has a non-NaN score.
*
* @param type
* @param positional
* @return
*/
float getMaximumScore(String type, boolean positional);
/**
* 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();
}