package jalview.datamodel.features;

import jalview.datamodel.SequenceFeature;

import java.util.ArrayList;
import java.util.Collections;
import java.util.HashMap;
import java.util.List;
import java.util.Map;

/**
 * A class that stores sequence features in a way that supports efficient
 * querying by type and location (overlap). Intended for (but not limited to)
 * storage of features for one sequence.
 * 
 * @author gmcarstairs
 *
 */
public class SequenceFeatures
{

  /*
   * map from feature type to structured store of features for that type
   * null types are permitted (but not a good idea!)
   */
  private Map<String, FeatureStore> featureStore;

  /**
   * Constructor
   */
  public SequenceFeatures()
  {
    featureStore = new HashMap<String, FeatureStore>();
  }

  /**
   * 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 boolean add(SequenceFeature sf)
  {
    String type = sf.getType();

    if (featureStore.get(type) == null)
    {
      featureStore.put(type, new FeatureStore());
    }
    return featureStore.get(type).addFeature(sf);
  }

  /**
   * Returns a (possibly empty) list of features of the given type which overlap
   * the (inclusive) sequence position range
   * 
   * @param type
   * @param from
   * @param to
   * @return
   */
  public List<SequenceFeature> findFeatures(String type, int from,
          int to)
  {
    FeatureStore features = featureStore.get(type);
    if (features == null)
    {
      return Collections.emptyList();
    }
    return features.findOverlappingFeatures(from, to);
  }

  /**
   * Answers a list of all features stored (including non-positional), in no
   * particular guaranteed order
   * 
   * @return
   */
  public List<SequenceFeature> getFeatures()
  {
    List<SequenceFeature> result = new ArrayList<SequenceFeature>();
    for (FeatureStore featureSet : featureStore.values())
    {
      result.addAll(featureSet.getFeatures());
    }
    return result;
  }

  /**
   * Answers a list of all non-positional features stored, in no particular
   * guaranteed order
   * 
   * @return
   */
  public List<SequenceFeature> getNonPositionalFeatures()
  {
    List<SequenceFeature> result = new ArrayList<SequenceFeature>();
    for (FeatureStore featureSet : featureStore.values())
    {
      result.addAll(featureSet.getNonPositionalFeatures());
    }
    return result;
  }

  /**
   * Answers a list of all contact features stored, in no particular guaranteed
   * order
   * 
   * @return
   */
  public List<SequenceFeature> getContactFeatures()
  {
    List<SequenceFeature> result = new ArrayList<SequenceFeature>();
    for (FeatureStore featureSet : featureStore.values())
    {
      result.addAll(featureSet.getContactFeatures());
    }
    return result;
  }

  /**
   * Answers a list of all features of the given type (including
   * non-positional), in no particular guaranteed order
   * 
   * @return
   */
  public List<SequenceFeature> getFeatures(String type)
  {
    List<SequenceFeature> result = new ArrayList<SequenceFeature>();
    FeatureStore featureSet = featureStore.get(type);
    if (featureSet != null)
    {
      result.addAll(featureSet.getFeatures());
    }
    return result;
  }

  /**
   * Answers a list of all contact features of the given type, in no particular
   * guaranteed order
   * 
   * @return
   */
  public List<SequenceFeature> getContactFeatures(String type)
  {
    List<SequenceFeature> result = new ArrayList<SequenceFeature>();
    FeatureStore featureSet = featureStore.get(type);
    if (featureSet != null)
    {
      result.addAll(featureSet.getContactFeatures());
    }
    return result;
  }

  /**
   * Answers a list of all non-positional features of the given type, in no
   * particular guaranteed order
   * 
   * @return
   */
  public List<SequenceFeature> getNonPositionalFeatures(String type)
  {
    List<SequenceFeature> result = new ArrayList<SequenceFeature>();
    FeatureStore featureSet = featureStore.get(type);
    if (featureSet != null)
    {
      result.addAll(featureSet.getNonPositionalFeatures());
    }
    return result;
  }

  /**
   * 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 boolean delete(SequenceFeature sf)
  {
    for (FeatureStore featureSet : featureStore.values())
    {
      if (featureSet.delete(sf))
      {
        return true;
      }
    }
    return false;
  }

  /**
   * Answers true if this store contains at least one feature, else false
   * 
   * @return
   */
  public boolean hasFeatures()
  {
    for (FeatureStore featureSet : featureStore.values())
    {
      if (!featureSet.isEmpty())
      {
        return true;
      }
    }
    return false;
  }
}