+/*
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
+ *
+ * This file is part of Jalview.
+ *
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
+ *
+ * Jalview is distributed in the hope that it will be useful, but
+ * WITHOUT ANY WARRANTY; without even the implied warranty
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
+ * PURPOSE. See the GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
package jalview.datamodel.features;
import jalview.datamodel.SequenceFeature;
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, 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<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
* @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();
+
+ /**
+ * Answers a (possibly empty) list of features of the specified type that
+ * overlap the specified column position. If parameter {@code result} is not
+ * null, features are appended to it and the (possibly extended) list is
+ * returned.
+ *
+ * @param pos
+ * @param type
+ * @param result
+ * @return
+ */
+ List<SequenceFeature> findFeatures(int pos, String type, List<SequenceFeature> result);
+
+ /**
+ * Answers true if there are any features of the given type, else false
+ */
+ boolean hasFeatures(String type);
+}