package jalview.datamodel.features;

import jalview.datamodel.ContiguousI;
import jalview.datamodel.SequenceFeature;
import jalview.io.gff.SequenceOntologyFactory;
import jalview.io.gff.SequenceOntologyI;

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

/**
 * 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
{
  /**
   * a comparator for sorting features by start position ascending
   */
  private static Comparator<ContiguousI> FORWARD_STRAND = new Comparator<ContiguousI>()
  {
    @Override
    public int compare(ContiguousI o1, ContiguousI o2)
    {
      return Integer.compare(o1.getBegin(), o2.getBegin());
    }
  };

  /**
   * a comparator for sorting features by end position descending
   */
  private static Comparator<ContiguousI> REVERSE_STRAND = new Comparator<ContiguousI>()
  {
    @Override
    public int compare(ContiguousI o1, ContiguousI o2)
    {
      return Integer.compare(o2.getEnd(), o1.getEnd());
    }
  };

  /*
   * 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()
  {
    /*
     * use a TreeMap so that features are returned in alphabetical order of type
     * ? wrap as a synchronized map for add and delete operations
     */
    // featureStore = Collections
    // .synchronizedSortedMap(new TreeMap<String, FeatureStore>());
    featureStore = new TreeMap<String, FeatureStore>();
  }

  /**
   * Constructor given a list of features
   */
  public SequenceFeatures(List<SequenceFeature> features)
  {
    this();
    if (features != null)
    {
      for (SequenceFeature feature : features)
      {
        add(feature);
      }
    }
  }

  /**
   * {@inheritDoc}
   */
  @Override
  public boolean add(SequenceFeature sf)
  {
    String type = sf.getType();
    if (type == null)
    {
      System.err.println("Feature type may not be null: " + sf.toString());
      return false;
    }

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

  /**
   * {@inheritDoc}
   */
  @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;
  }

  /**
   * {@inheritDoc}
   */
  @Override
  public List<SequenceFeature> getAllFeatures(String... type)
  {
    List<SequenceFeature> result = new ArrayList<SequenceFeature>();

    result.addAll(getPositionalFeatures(type));

    result.addAll(getNonPositionalFeatures());

    return result;
  }

  /**
   * {@inheritDoc}
   */
  @Override
  public List<SequenceFeature> getFeaturesByOntology(String... ontologyTerm)
  {
    if (ontologyTerm == null || ontologyTerm.length == 0)
    {
      return new ArrayList<SequenceFeature>();
    }

    Set<String> featureTypes = getFeatureTypes(ontologyTerm);
    return getAllFeatures(featureTypes.toArray(new String[featureTypes
            .size()]));
  }

  /**
   * {@inheritDoc}
   */
  @Override
  public int getFeatureCount(boolean positional, String... type)
  {
    int result = 0;

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

  /**
   * {@inheritDoc}
   */
  @Override
  public int getTotalFeatureLength(String... type)
  {
    int result = 0;

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

  }

  /**
   * {@inheritDoc}
   */
  @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)
  {
    if (type == null || type.length == 0)
    {
      /*
       * no vararg parameter supplied
       */
      return featureStore.keySet();
    }

    /*
     * else make a copy of the list, and remove any null value just in case,
     * as it would cause errors looking up the features Map
     * sort in alphabetical order for consistent output behaviour
     */
    List<String> types = new ArrayList<String>(Arrays.asList(type));
    types.remove(null);
    Collections.sort(types);
    return types;
  }

  /**
   * {@inheritDoc}
   */
  @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;
  }

  /**
   * {@inheritDoc}
   */
  @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;
  }

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

  /**
   * {@inheritDoc}
   */
  @Override
  public boolean hasFeatures()
  {
    for (FeatureStore featureSet : featureStore.values())
    {
      if (!featureSet.isEmpty())
      {
        return true;
      }
    }
    return false;
  }

  /**
   * {@inheritDoc}
   */
  @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;
  }

  /**
   * {@inheritDoc}
   */
  @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;
  }

  /**
   * {@inheritDoc}
   */
  @Override
  public Set<String> getFeatureTypes(String... soTerm)
  {
    Set<String> types = new HashSet<String>();
    for (Entry<String, FeatureStore> entry : featureStore.entrySet())
    {
      String type = entry.getKey();
      if (!entry.getValue().isEmpty() && isOntologyTerm(type, soTerm))
      {
        types.add(type);
      }
    }
    return types;
  }

  /**
   * Answers true if the given type is one of the specified sequence ontology
   * terms (or a sub-type of one), or if no terms are supplied. Answers false if
   * filter terms are specified and the given term does not match any of them.
   * 
   * @param type
   * @param soTerm
   * @return
   */
  protected boolean isOntologyTerm(String type, String... soTerm)
  {
    if (soTerm == null || soTerm.length == 0)
    {
      return true;
    }
    SequenceOntologyI so = SequenceOntologyFactory.getInstance();
    for (String term : soTerm)
    {
      if (so.isA(type, term))
      {
        return true;
      }
    }
    return false;
  }

  /**
   * {@inheritDoc}
   */
  @Override
  public float getMinimumScore(String type, boolean positional)
  {
    return featureStore.containsKey(type) ? featureStore.get(type)
            .getMinimumScore(positional) : Float.NaN;
  }

  /**
   * {@inheritDoc}
   */
  @Override
  public float getMaximumScore(String type, boolean positional)
  {
    return featureStore.containsKey(type) ? featureStore.get(type)
            .getMaximumScore(positional) : Float.NaN;
  }

  /**
   * A convenience method to sort features by start position ascending (if on
   * forward strand), or end position descending (if on reverse strand)
   * 
   * @param features
   * @param forwardStrand
   */
  public static void sortFeatures(List<SequenceFeature> features,
          final boolean forwardStrand)
  {
    Collections.sort(features, forwardStrand ? FORWARD_STRAND
            : REVERSE_STRAND);
  }

  /**
   * {@inheritDoc} This method is 'semi-optimised': it only inspects features
   * for types that include the specified group, but has to inspect every
   * feature of those types for matching feature group. This is efficient unless
   * a sequence has features that share the same type but are in different
   * groups - an unlikely case.
   * <p>
   * For example, if RESNUM feature is created with group = PDBID, then features
   * would only be retrieved for those sequences associated with the target
   * PDBID (group).
   */
  @Override
  public List<SequenceFeature> getFeaturesForGroup(boolean positional,
          String group, String... type)
  {
    List<SequenceFeature> result = new ArrayList<SequenceFeature>();
    Iterable<String> types = varargToTypes(type);

    for (String featureType : types)
    {
      /*
       * check whether the feature type is present, and also
       * whether it has features for the specified group
       */
      FeatureStore features = featureStore.get(featureType);
      if (features != null
              && features.getFeatureGroups(positional).contains(group))
      {
        result.addAll(features.getFeaturesForGroup(positional, group));
      }
    }
    return result;
  }

  /**
   * {@inheritDoc}
   */
  @Override
  public boolean shiftFeatures(int shift)
  {
    boolean modified = false;
    for (FeatureStore fs : featureStore.values())
    {
      modified |= fs.shiftFeatures(shift);
    }
    return modified;
  }
}