* Adds one sequence feature to the store, and returns true, unless the
* feature is already contained in the store, in which case this method
* returns false. Containment is determined by SequenceFeature.equals()
- * comparison.
+ * comparison. Answers false, and does not add the feature, if feature type is
+ * null.
*
* @param sf
*/
- public abstract boolean add(SequenceFeature sf);
+ boolean add(SequenceFeature sf);
/**
* Returns a (possibly empty) list of features, optionally restricted to
* @param type
* @return
*/
- public abstract List<SequenceFeature> findFeatures(int from, int to,
+ List<SequenceFeature> findFeatures(int from, int to,
String... type);
/**
- * Answers a list of all features stored, optionally restricted to specified
- * types, in no particular guaranteed order
+ * 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.
+ * <p>
+ * To filter non-positional features by type, use
+ * getNonPositionalFeatures(type).
+ *
+ * @param type
+ * @return
+ */
+ 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.
+ *
+ * @param ontologyTerm
* @return
*/
- public abstract List<SequenceFeature> getAllFeatures(String... type);
+ List<SequenceFeature> getFeaturesByOntology(String... ontologyTerm);
- public abstract int getFeatureCount(boolean positional, String... type);
+ /**
+ * 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
* @param type
* @return
*/
- public abstract List<SequenceFeature> getPositionalFeatures(
+ List<SequenceFeature> getPositionalFeatures(
String... type);
/**
*
* @return
*/
- public abstract List<SequenceFeature> getContactFeatures(String... type);
+ List<SequenceFeature> getContactFeatures(String... type);
/**
* Answers a list of all non-positional features, optionally restricted to
* if no type is specified, all are returned
* @return
*/
- public abstract List<SequenceFeature> getNonPositionalFeatures(
+ List<SequenceFeature> getNonPositionalFeatures(
String... type);
/**
*
* @param sf
*/
- public abstract boolean delete(SequenceFeature sf);
+ boolean delete(SequenceFeature sf);
/**
* Answers true if this store contains at least one feature, else false
*
* @return
*/
- public abstract boolean hasFeatures();
+ boolean hasFeatures();
/**
* Returns a set of the distinct feature groups present in the collection. The
* @param type
* @return
*/
- public abstract Set<String> getFeatureGroups(boolean positionalFeatures,
+ Set<String> getFeatureGroups(boolean positionalFeatures,
String... type);
/**
* @param groups
* @return
*/
- public abstract Set<String> getFeatureTypesForGroups(
+ Set<String> getFeatureTypesForGroups(
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(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
*/
- public abstract Set<String> getFeatureTypes();
+ 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,
+ * returning true if at least one feature was shifted, else false
+ *
+ * @param shift
+ */
+ abstract boolean shiftFeatures(int shift);
}
\ No newline at end of file