package jalview.datamodel.features;

import jalview.datamodel.SequenceFeature;

import java.util.ArrayList;
import java.util.Arrays;
import java.util.Collections;
import java.util.HashMap;
import java.util.HashSet;
import java.util.List;
import java.util.Map;
import java.util.Map.Entry;
import java.util.Set;

/**
 * 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 implements SequenceFeaturesI
{

  /*
   * 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>();
  }

  /* (non-Javadoc)
   * @see jalview.datamodel.features.SequenceFeaturesI#add(jalview.datamodel.SequenceFeature)
   */
  @Override
  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);
  }

  /* (non-Javadoc)
   * @see jalview.datamodel.features.SequenceFeaturesI#findFeatures(int, int, java.lang.String)
   */
  @Override
  public List<SequenceFeature> findFeatures(int from, int to,
          String... type)
  {
    List<SequenceFeature> result = new ArrayList<SequenceFeature>();

    for (String featureType : varargToTypes(type))
    {
      FeatureStore features = featureStore.get(featureType);
      if (features != null)
      {
        result.addAll(features.findOverlappingFeatures(from, to));
      }
    }

    return result;
  }

  /* (non-Javadoc)
   * @see jalview.datamodel.features.SequenceFeaturesI#getAllFeatures(java.lang.String)
   */
  @Override
  public List<SequenceFeature> getAllFeatures(String... type)
  {
    List<SequenceFeature> result = new ArrayList<SequenceFeature>();

    result.addAll(getPositionalFeatures(type));

    result.addAll(getNonPositionalFeatures(type));

    return result;
  }

  /* (non-Javadoc)
   * @see jalview.datamodel.features.SequenceFeaturesI#getFeatureCount(boolean, java.lang.String)
   */
  @Override
  public int getFeatureCount(boolean positional, String... type)
  {
    int result = 0;
    for (FeatureStore fs : featureStore.values())
    {
      result += fs.size(positional);
    }

    return result;
  }

  /* (non-Javadoc)
   * @see jalview.datamodel.features.SequenceFeaturesI#getPositionalFeatures(java.lang.String)
   */
  @Override
  public List<SequenceFeature> getPositionalFeatures(String... type)
  {
    List<SequenceFeature> result = new ArrayList<SequenceFeature>();

    for (String featureType : varargToTypes(type))
    {
      FeatureStore featureSet = featureStore.get(featureType);
      if (featureSet != null)
      {
        result.addAll(featureSet.getPositionalFeatures());
      }
    }
    return result;
  }

  /**
   * A convenience method that converts a vararg for feature types to an
   * Iterable, replacing the value with the stored feature types if it is null
   * or empty
   * 
   * @param type
   * @return
   */
  protected Iterable<String> varargToTypes(String... type)
  {
    return type == null || type.length == 0 ? featureStore
            .keySet() : Arrays.asList(type);
  }

  /* (non-Javadoc)
   * @see jalview.datamodel.features.SequenceFeaturesI#getContactFeatures(java.lang.String)
   */
  @Override
  public List<SequenceFeature> getContactFeatures(String... type)
  {
    List<SequenceFeature> result = new ArrayList<SequenceFeature>();

    for (String featureType : varargToTypes(type))
    {
      FeatureStore featureSet = featureStore.get(featureType);
      if (featureSet != null)
      {
        result.addAll(featureSet.getContactFeatures());
      }
    }
    return result;
  }

  /* (non-Javadoc)
   * @see jalview.datamodel.features.SequenceFeaturesI#getNonPositionalFeatures(java.lang.String)
   */
  @Override
  public List<SequenceFeature> getNonPositionalFeatures(String... type)
  {
    List<SequenceFeature> result = new ArrayList<SequenceFeature>();

    for (String featureType : varargToTypes(type))
    {
      FeatureStore featureSet = featureStore.get(featureType);
      if (featureSet != null)
      {
        result.addAll(featureSet.getNonPositionalFeatures());
      }
    }
    return result;
  }

  /* (non-Javadoc)
   * @see jalview.datamodel.features.SequenceFeaturesI#delete(jalview.datamodel.SequenceFeature)
   */
  @Override
  public boolean delete(SequenceFeature sf)
  {
    for (FeatureStore featureSet : featureStore.values())
    {
      if (featureSet.delete(sf))
      {
        return true;
      }
    }
    return false;
  }

  /* (non-Javadoc)
   * @see jalview.datamodel.features.SequenceFeaturesI#hasFeatures()
   */
  @Override
  public boolean hasFeatures()
  {
    for (FeatureStore featureSet : featureStore.values())
    {
      if (!featureSet.isEmpty())
      {
        return true;
      }
    }
    return false;
  }

  /* (non-Javadoc)
   * @see jalview.datamodel.features.SequenceFeaturesI#getFeatureGroups(boolean, java.lang.String)
   */
  @Override
  public Set<String> getFeatureGroups(boolean positionalFeatures,
          String... type)
  {
    Set<String> groups = new HashSet<String>();

    Iterable<String> types = varargToTypes(type);

    for (String featureType : types)
    {
      FeatureStore featureSet = featureStore.get(featureType);
      if (featureSet != null)
      {
        groups.addAll(featureSet.getFeatureGroups(positionalFeatures));
      }
    }

    return groups;
  }

  /* (non-Javadoc)
   * @see jalview.datamodel.features.SequenceFeaturesI#getFeatureTypesForGroups(boolean, java.lang.String)
   */
  @Override
  public Set<String> getFeatureTypesForGroups(boolean positionalFeatures,
          String... groups)
  {
    Set<String> result = new HashSet<String>();

    for (Entry<String, FeatureStore> featureType : featureStore.entrySet())
    {
      Set<String> featureGroups = featureType.getValue().getFeatureGroups(
              positionalFeatures);
      for (String group : groups)
      {
        if (featureGroups.contains(group))
        {
          /*
           * yes this feature type includes one of the query groups
           */
          result.add(featureType.getKey());
          break;
        }
      }
    }

    return result;
  }

  /* (non-Javadoc)
   * @see jalview.datamodel.features.SequenceFeaturesI#getFeatureTypes()
   */
  @Override
  public Set<String> getFeatureTypes()
  {
    return Collections.unmodifiableSet(featureStore.keySet());
  }
}