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.
+ *
+ * To filter non-positional features by type, use
+ * getNonPositionalFeatures(type).
*
* @param type
* @return
*/
- public abstract List getAllFeatures(String... type);
+ 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);
- 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
@@ -49,7 +117,7 @@ public interface SequenceFeaturesI
* @param type
* @return
*/
- public abstract List getPositionalFeatures(
+ List getPositionalFeatures(
String... type);
/**
@@ -58,7 +126,7 @@ public interface SequenceFeaturesI
*
* @return
*/
- public abstract List getContactFeatures(String... type);
+ List getContactFeatures(String... type);
/**
* Answers a list of all non-positional features, optionally restricted to
@@ -68,7 +136,7 @@ public interface SequenceFeaturesI
* if no type is specified, all are returned
* @return
*/
- public abstract List getNonPositionalFeatures(
+ List getNonPositionalFeatures(
String... type);
/**
@@ -79,14 +147,14 @@ public interface SequenceFeaturesI
*
* @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
@@ -99,7 +167,7 @@ public interface SequenceFeaturesI
* @param type
* @return
*/
- public abstract Set getFeatureGroups(boolean positionalFeatures,
+ Set getFeatureGroups(boolean positionalFeatures,
String... type);
/**
@@ -112,14 +180,52 @@ public interface SequenceFeaturesI
* @param groups
* @return
*/
- public abstract Set getFeatureTypesForGroups(
+ Set getFeatureTypesForGroups(
boolean positionalFeatures, String... groups);
/**
- * Answers an immutable 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
*/
- public abstract Set getFeatureTypes();
+ Set getFeatureTypes(String... soTerm);
-}
\ No newline at end of file
+ /**
+ * 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();
+}