/* * 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 . * The Jalview Authors are detailed in the 'AUTHORS' file. */ package jalview.datamodel.features; import jalview.datamodel.SequenceFeature; import java.util.List; import java.util.Set; public interface SequenceFeaturesI { /** * 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. Answers false, and does not add the feature, if feature type is * null. * * @param sf */ boolean add(SequenceFeature sf); /** * Returns a (possibly empty) list of features, optionally restricted to * specified types, which overlap the given (inclusive) sequence position * range * * @param from * @param to * @param type * @return */ List findFeatures(int from, int to, String... type); /** * 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 */ 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); /** * 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 * specified types, in no particular guaranteed order * * @param type * @return */ List getPositionalFeatures( String... type); /** * Answers a list of all contact features, optionally restricted to specified * types, in no particular guaranteed order * * @return */ List getContactFeatures(String... type); /** * Answers a list of all non-positional features, optionally restricted to * specified types, in no particular guaranteed order * * @param type * if no type is specified, all are returned * @return */ List getNonPositionalFeatures( String... type); /** * Deletes the given feature from the store, returning true if it was found * (and deleted), else false. This method makes no assumption that the feature * is in the 'expected' place in the store, in case it has been modified since * it was added. * * @param sf */ boolean delete(SequenceFeature sf); /** * Answers true if this store contains at least one feature, else false * * @return */ boolean hasFeatures(); /** * Returns a set of the distinct feature groups present in the collection. The * set may include null. The boolean parameter determines whether the groups * for positional or for non-positional features are returned. The optional * type parameter may be used to restrict to groups for specified feature * types. * * @param positionalFeatures * @param type * @return */ Set getFeatureGroups(boolean positionalFeatures, String... type); /** * Answers the set of distinct feature types for which there is at least one * feature with one of the given feature group(s). The boolean parameter * determines whether the groups for positional or for non-positional features * are returned. * * @param positionalFeatures * @param groups * @return */ Set getFeatureTypesForGroups( boolean positionalFeatures, String... groups); /** * 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 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 */ 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); }