+/*
+ * 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;
/**
* Returns a (possibly empty) list of features, optionally restricted to
* specified types, which overlap the given (inclusive) sequence position
- * range
+ * range. If types are specified, features are returned in the order of the
+ * types given.
*
* @param from
* @param to
* @param type
* @return
*/
- List<SequenceFeature> findFeatures(int from, int to,
- String... type);
+ List<SequenceFeature> findFeatures(int from, int to, String... type);
/**
* Answers a list of all features stored, in no particular guaranteed order.
List<SequenceFeature> getAllFeatures(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.
+ * 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
* @param type
* @return
*/
- List<SequenceFeature> getPositionalFeatures(
- String... type);
+ List<SequenceFeature> getPositionalFeatures(String... type);
/**
* Answers a list of all contact features, optionally restricted to specified
* if no type is specified, all are returned
* @return
*/
- List<SequenceFeature> getNonPositionalFeatures(
- String... type);
+ List<SequenceFeature> getNonPositionalFeatures(String... type);
/**
* Deletes the given feature from the store, returning true if it was found
* @param type
* @return
*/
- Set<String> getFeatureGroups(boolean positionalFeatures,
- String... type);
+ Set<String> getFeatureGroups(boolean positionalFeatures, String... type);
/**
* Answers the set of distinct feature types for which there is at least one
* @param groups
* @return
*/
- Set<String> getFeatureTypesForGroups(
- boolean positionalFeatures, String... groups);
+ Set<String> getFeatureTypesForGroups(boolean positionalFeatures,
+ String... groups);
/**
* Answers a set of the distinct feature types for which a feature is stored.
* @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();
+}