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.
   * 
   * @param sf
   */
  public abstract 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
   */
  public abstract 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
   * 
   * @param type
   * @return
   */
  public abstract List<SequenceFeature> getAllFeatures(String... type);

  public abstract int getFeatureCount(boolean positional, String... type);

  /**
   * Answers a list of all positional features, optionally restricted to
   * specified types, in no particular guaranteed order
   * 
   * @param type
   * @return
   */
  public abstract List<SequenceFeature> getPositionalFeatures(
          String... type);

  /**
   * Answers a list of all contact features, optionally restricted to specified
   * types, in no particular guaranteed order
   * 
   * @return
   */
  public abstract List<SequenceFeature> 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
   */
  public abstract List<SequenceFeature> 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
   */
  public abstract boolean delete(SequenceFeature sf);

  /**
   * Answers true if this store contains at least one feature, else false
   * 
   * @return
   */
  public abstract 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
   */
  public abstract Set<String> 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
   */
  public abstract Set<String> getFeatureTypesForGroups(
          boolean positionalFeatures, String... groups);

  /**
   * Answers an immutable set of the distinct feature types for which a feature
   * is stored
   * @return
   */
  public abstract Set<String> getFeatureTypes();

}