package jalview.datamodel.features;

import jalview.datamodel.SequenceFeature;

import java.util.Collection;
import java.util.List;
import java.util.Set;

public interface FeatureStoreI
{

  boolean addFeature(SequenceFeature feature);

  boolean contains(SequenceFeature feature);

  boolean delete(SequenceFeature sf);

  List<SequenceFeature> findOverlappingFeatures(long start, long end);

  List<SequenceFeature> findOverlappingFeatures(long start, long end,
          List<SequenceFeature> result);

  List<SequenceFeature> getContactFeatures();

  List<SequenceFeature> getContactFeatures(List<SequenceFeature> result);

  int getFeatureCount(boolean positional);

  Set<String> getFeatureGroups(boolean positionalFeatures);

  Collection<SequenceFeature> getFeatures();

  List<SequenceFeature> getFeaturesForGroup(boolean positional,
          String group);

  float getMaximumScore(boolean positional);

  float getMinimumScore(boolean positional);

  List<SequenceFeature> getNonPositionalFeatures();

  List<SequenceFeature> getNonPositionalFeatures(
          List<SequenceFeature> result);

  List<SequenceFeature> getPositionalFeatures();

  List<SequenceFeature> getPositionalFeatures(List<SequenceFeature> result);

  int getTotalFeatureLength();

  boolean isEmpty();

  boolean shiftFeatures(int fromPosition, int shiftBy);

  boolean listContains(List<SequenceFeature> features,
          SequenceFeature feature);

}