+/*
+ * 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;
* 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
*/
- public abstract List<SequenceFeature> getAllFeatures(String... type);
+ List<SequenceFeature> getAllFeatures(String... type);
- public abstract int getFeatureCount(boolean positional, 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.
+ *
+ * @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
*/
- public abstract Set<String> getFeatureTypes();
+ Set<String> 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();
+}
git://source.jalview.org / jalview.git / blobdiff