/*
 * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
 * Copyright (C) $$Year-Rel$$ The Jalview Authors
 * 
 * This file is part of Jalview.
 * 
 * Jalview is free software: you can redistribute it and/or
 * modify it under the terms of the GNU General Public License 
 * as published by the Free Software Foundation, either version 3
 * of the License, or (at your option) any later version.
 *  
 * Jalview is distributed in the hope that it will be useful, but 
 * WITHOUT ANY WARRANTY; without even the implied warranty 
 * of MERCHANTABILITY or FITNESS FOR A PARTICULAR 
 * PURPOSE.  See the GNU General Public License for more details.
 * 
 * You should have received a copy of the GNU General Public License
 * along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
 * The Jalview Authors are detailed in the 'AUTHORS' file.
 */
package jalview.datamodel.features;

import jalview.datamodel.SequenceFeature;
import jalview.util.Platform;

import java.util.ArrayList;
import java.util.Collection;
import java.util.Collections;
import java.util.HashSet;
import java.util.List;
import java.util.Set;

import intervalstore.api.IntervalStoreI;

public abstract class FeatureStore implements FeatureStoreI
{

  /**
   * track last start for quick insertion of ordered features
   */
  protected int lastStart = -1;

  protected int lastContactStart = -1;

  /*
   * Non-positional features have no (zero) start/end position.
   * Kept as a separate list in case this criterion changes in future.
   */
  List<SequenceFeature> nonPositionalFeatures;

  /*
   * contact features ordered by first contact position
   */
  List<SequenceFeature> contactFeatureStarts;

  /*
   * contact features ordered by second contact position
   */
  List<SequenceFeature> contactFeatureEnds;

  /*
   * IntervalStore holds remaining features and provides efficient
   * query for features overlapping any given interval
   */
  IntervalStoreI<SequenceFeature> features;

  /*
   * Feature groups represented in stored positional features 
   * (possibly including null)
   */
  Set<String> positionalFeatureGroups;

  /*
   * Feature groups represented in stored non-positional features 
   * (possibly including null)
   */
  Set<String> nonPositionalFeatureGroups;

  /*
   * the total length of all positional features; contact features count 1 to
   * the total and 1 to size(), consistent with an average 'feature length' of 1
   */
  int totalExtent;

  float positionalMinScore;

  float positionalMaxScore;

  float nonPositionalMinScore;

  float nonPositionalMaxScore;

  public final static int INTERVAL_STORE_DEFAULT = -1;

  /**
   * original NCList-based IntervalStore
   */
  public final static int INTERVAL_STORE_NCLIST_OBJECT = 0;

  /**
   * linked-list IntervalStore
   */
  public final static int INTERVAL_STORE_LINKED_LIST_PRESORT = 1;

  /**
   * linked-list IntervalStore
   */
  public final static int INTERVAL_STORE_LINKED_LIST_NO_PRESORT = 2;

  /**
   * NCList as array buffer IntervalStore
   */
  public final static int INTERVAL_STORE_NCLIST_BUFFER_PRESORT = 3;

  /**
   * NCList as array buffer IntervalStore
   */
  public final static int INTERVAL_STORE_NCLIST_BUFFER_NO_PRESORT = 4;

  static final int intervalStoreJavaOption = INTERVAL_STORE_NCLIST_OBJECT;

  static final int intervalStoreJSOption = INTERVAL_STORE_NCLIST_BUFFER_PRESORT;

  /**
   * Answers the 'length' of the feature, counting 0 for non-positional features
   * and 1 for contact features
   * 
   * @param feature
   * @return
   */
  protected static int getFeatureLength(SequenceFeature feature)
  {
    if (feature.isNonPositional())
    {
      return 0;
    }
    if (feature.isContactFeature())
    {
      return 1;
    }
    return 1 + feature.getEnd() - feature.getBegin();
  }

  /**
   * Answers true if the list contains the feature, else false. This method is
   * optimised for the condition that the list is sorted on feature start
   * position ascending, and will give unreliable results if this does not hold.
   * 
   * @param list
   * @param feature
   * @return
   */
  @Override
  public boolean listContains(List<SequenceFeature> list,
          SequenceFeature feature)
  {
    if (list == null || feature == null)
    {
      return false;
    }

    return (getEquivalentFeatureIndex(list, feature) >= 0);
  }

  /**
   * Binary search for the index (&gt;= 0) of a feature in a list.
   * 
   * @param list
   * @param feature
   * @return index if found; -1 if not
   */
  protected int getEquivalentFeatureIndex(List<SequenceFeature> list,
          SequenceFeature feature)
  {

    /*
     * locate the first entry in the list which does not precede the feature
     */
    int begin = feature.begin;
    int pos = findFirstBegin(list, begin);
    int len = list.size();
    while (pos < len)
    {
      SequenceFeature sf = list.get(pos);
      if (sf.begin > begin)
      {
        return -1; // no match found
      }
      if (sf.equals(feature))
      {
        return pos;
      }
      pos++;
    }
    return -1;
  }

  /**
   * A helper method to return the maximum of two floats, where a non-NaN value
   * is treated as 'greater than' a NaN value (unlike Math.max which does the
   * opposite)
   * 
   * @param f1
   * @param f2
   */
  protected static float max(float f1, float f2)
  {
    if (Float.isNaN(f1))
    {
      return Float.isNaN(f2) ? f1 : f2;
    }
    else
    {
      return Float.isNaN(f2) ? f1 : Math.max(f1, f2);
    }
  }

  /**
   * A helper method to return the minimum of two floats, where a non-NaN value
   * is treated as 'less than' a NaN value (unlike Math.min which does the
   * opposite)
   * 
   * @param f1
   * @param f2
   */
  protected static float min(float f1, float f2)
  {
    if (Float.isNaN(f1))
    {
      return Float.isNaN(f2) ? f1 : f2;
    }
    else
    {
      return Float.isNaN(f2) ? f1 : Math.min(f1, f2);
    }
  }

  /**
   * standard constructor
   */
  public FeatureStore()
  {
    this(INTERVAL_STORE_DEFAULT);
  }

  /**
   * constructor for testing only
   */
  public FeatureStore(int intervalStoreType)
  {
    features = getIntervalStore(intervalStoreType);
    positionalFeatureGroups = new HashSet<>();
    nonPositionalFeatureGroups = new HashSet<>();
    positionalMinScore = Float.NaN;
    positionalMaxScore = Float.NaN;
    nonPositionalMinScore = Float.NaN;
    nonPositionalMaxScore = Float.NaN;

    // we only construct nonPositionalFeatures, contactFeatures if we need to
  }

  private IntervalStoreI<SequenceFeature> getIntervalStore(int type)
  {
    switch (type != INTERVAL_STORE_DEFAULT ? type : //
    Platform.isJS() //
            ? intervalStoreJSOption
            : intervalStoreJavaOption)
    {
    default:
    case INTERVAL_STORE_NCLIST_OBJECT:
      return new intervalstore.impl.IntervalStore<>();
    case INTERVAL_STORE_NCLIST_BUFFER_PRESORT:
      return new intervalstore.nonc.IntervalStore<>(true);
    case INTERVAL_STORE_NCLIST_BUFFER_NO_PRESORT:
      return new intervalstore.nonc.IntervalStore<>(false);
    case INTERVAL_STORE_LINKED_LIST_PRESORT:
      return new intervalstore.nonc.IntervalStore0<>(true);
    case INTERVAL_STORE_LINKED_LIST_NO_PRESORT:
      return new intervalstore.nonc.IntervalStore0<>(false);
    }
  }

  /**
   * Add a contact feature to the lists that hold them ordered by start (first
   * contact) and by end (second contact) position, ensuring the lists remain
   * ordered, and returns true. This method allows duplicate features to be
   * added, so test before calling to avoid this.
   * 
   * @param feature
   * @return
   */
  protected synchronized boolean addContactFeature(SequenceFeature feature)
  {
    if (contactFeatureStarts == null)
    {
      contactFeatureStarts = new ArrayList<>();
      contactFeatureEnds = new ArrayList<>();
    }

    /*
     * insert into list sorted by start (first contact position):
     * binary search the sorted list to find the insertion point
     */
    contactFeatureStarts.add(
            findFirstBegin(contactFeatureStarts, feature.begin), feature);
    /*
     * insert into list sorted by end (second contact position):
     * binary search the sorted list to find the insertion point
     */
    contactFeatureEnds.add(findFirstEnd(contactFeatureEnds, feature.end),
            feature);

    return true;
  }

  /**
   * 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 feature
   */

  @Override
  public boolean addFeature(SequenceFeature feature)
  {
    // if (contains(feature))
    // {
    // return false;
    // }

    // /*
    // * keep a record of feature groups
    // */
    // if (!feature.isNonPositional())
    // {
    // positionalFeatureGroups.add(feature.getFeatureGroup());
    // }

    if (feature.isContactFeature())
    {
      if (containsContactFeature(feature))
      {
        return false;
      }
      positionalFeatureGroups.add(feature.getFeatureGroup());
      if (feature.begin > lastContactStart)
      {
        lastContactStart = feature.begin;
      }
      addContactFeature(feature);
    }
    else if (feature.isNonPositional())
    {
      if (containsNonPositional(feature))
      {
        return false;
      }

      addNonPositionalFeature(feature);
    }
    else
    {
      // allow for check with
      if (checkContainsPositionalFeatureForAdd(feature)
              || !addPositionalFeature(feature))
      {
        return false;
      }
      positionalFeatureGroups.add(feature.getFeatureGroup());
      if (feature.begin > lastStart)
      {
        lastStart = feature.begin;
      }
    }

    /*
     * record the total extent of positional features, to make
     * getTotalFeatureLength possible; we count the length of a 
     * contact feature as 1
     */
    totalExtent += getFeatureLength(feature);

    /*
     * record the minimum and maximum score for positional
     * and non-positional features
     */
    float score = feature.getScore();
    if (!Float.isNaN(score))
    {
      if (feature.isNonPositional())
      {
        nonPositionalMinScore = min(nonPositionalMinScore, score);
        nonPositionalMaxScore = max(nonPositionalMaxScore, score);
      }
      else
      {
        positionalMinScore = min(positionalMinScore, score);
        positionalMaxScore = max(positionalMaxScore, score);
      }
    }

    return true;
  }

  private void addFeaturesForGroup(String group,
          Collection<SequenceFeature> sfs, List<SequenceFeature> result)
  {
    if (sfs == null)
    {
      return;
    }
    for (SequenceFeature sf : sfs)
    {
      String featureGroup = sf.getFeatureGroup();
      if (group == null && featureGroup == null
              || group != null && group.equals(featureGroup))
      {
        result.add(sf);
      }
    }
  }

  /**
   * Adds one feature to the IntervalStore that can manage nested features
   * (creating the IntervalStore if necessary)
   * 
   * @return true if added -- allowing for late checking during addition
   */
  abstract protected boolean addPositionalFeature(SequenceFeature feature);

  /**
   * Adds the feature to the list of non-positional features (with lazy
   * instantiation of the list if it is null), and returns true. The feature
   * group is added to the set of distinct feature groups for non-positional
   * features. This method allows duplicate features, so test before calling to
   * prevent this.
   * 
   * @param feature
   */
  protected boolean addNonPositionalFeature(SequenceFeature feature)
  {
    if (nonPositionalFeatures == null)
    {
      nonPositionalFeatures = new ArrayList<>();
    }

    nonPositionalFeatures.add(feature);

    nonPositionalFeatureGroups.add(feature.getFeatureGroup());

    return true;
  }

  /**
   * Answers true if this store contains the given feature (testing by
   * SequenceFeature.equals), else false
   * 
   * @param feature
   * @return
   */
  @Override
  public boolean contains(SequenceFeature feature)
  {
    if (feature.isNonPositional())
    {
      return containsNonPositional(feature);

    }

    if (feature.isContactFeature())
    {
      return containsContactFeature(feature);

    }

    return containsPositionalFeature(feature);

  }

  /**
   * A check that can be overridden if the check is being done during the add
   * operation itself.
   * 
   * @param feature
   * @return
   */
  protected boolean checkContainsPositionalFeatureForAdd(
          SequenceFeature feature)
  {
    return containsPositionalFeature(feature);
  }

  private boolean containsPositionalFeature(SequenceFeature feature)
  {
    return features == null || feature.begin > lastStart ? false
            : containsFeature(feature);
  }

  private boolean containsContactFeature(SequenceFeature feature)
  {
    return contactFeatureStarts != null && feature.begin <= lastContactStart
            && listContains(contactFeatureStarts, feature);
  }

  private boolean containsNonPositional(SequenceFeature feature)
  {
    return nonPositionalFeatures == null ? false
            : nonPositionalFeatures.contains(feature);
  }

  abstract protected boolean containsFeature(SequenceFeature feature);

  /**
   * 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
   */

  @Override
  public synchronized boolean delete(SequenceFeature sf)
  {
    boolean removed = false;

    /*
     * try contact positions (and if found, delete
     * from both lists of contact positions)
     */
    if (!removed && contactFeatureStarts != null)
    {
      removed = contactFeatureStarts.remove(sf);
      if (removed)
      {
        contactFeatureEnds.remove(sf);
      }
    }

    /*
     * if not found, try non-positional features
     */
    if (!removed && nonPositionalFeatures != null)
    {
      removed = nonPositionalFeatures.remove(sf);
    }

    /*
     * if not found, try nested features
     */
    if (!removed && features != null)
    {
      removed = findAndRemoveNonContactFeature(sf);
    }

    if (removed)
    {
      rescanAfterDelete();
    }

    return removed;
  }

  abstract protected boolean findAndRemoveNonContactFeature(SequenceFeature sf);

  abstract protected void findContactFeatures(long from, long to,
          List<SequenceFeature> result);

  abstract protected int findFirstBegin(List<SequenceFeature> list,
          long pos);

  abstract protected int findFirstEnd(List<SequenceFeature> list, long pos);

  @Override
  public List<SequenceFeature> findOverlappingFeatures(long start, long end)
  {
    return findOverlappingFeatures(start, end, null);
  }

  @Override
  public List<SequenceFeature> getContactFeatures()
  {
    return getContactFeatures(new ArrayList<>());
  }

  /**
   * Answers a list of all contact features. If there are none, returns an
   * immutable empty list.
   * 
   * @return
   */

  @Override
  public List<SequenceFeature> getContactFeatures(
          List<SequenceFeature> result)
  {
    if (contactFeatureStarts != null)
    {
      result.addAll(contactFeatureStarts);
    }
    return result;
  }

  /**
   * Answers the number of positional (or non-positional) features stored.
   * Contact features count as 1.
   * 
   * @param positional
   * @return
   */

  @Override
  public int getFeatureCount(boolean positional)
  {
    if (!positional)
    {
      return nonPositionalFeatures == null ? 0
              : nonPositionalFeatures.size();
    }

    return (contactFeatureStarts == null ? 0 : contactFeatureStarts.size())
            + features.size();

  }

  /**
   * Answers the set of distinct feature groups stored, possibly including null,
   * as an unmodifiable view of the set. The parameter determines whether the
   * groups for positional or for non-positional features are returned.
   * 
   * @param positionalFeatures
   * @return
   */

  @Override
  public Set<String> getFeatureGroups(boolean positionalFeatures)
  {
    if (positionalFeatures)
    {
      return Collections.unmodifiableSet(positionalFeatureGroups);
    }
    else
    {
      return nonPositionalFeatureGroups == null
              ? Collections.<String> emptySet()
              : Collections.unmodifiableSet(nonPositionalFeatureGroups);
    }
  }

  @Override
  public Collection<SequenceFeature> getFeatures()
  {
    return features;
  }

  /**
   * Answers a list of all either positional or non-positional features whose
   * feature group matches the given group (which may be null)
   * 
   * @param positional
   * @param group
   * @return
   */

  @Override
  public List<SequenceFeature> getFeaturesForGroup(boolean positional,
          String group)
  {
    List<SequenceFeature> result = new ArrayList<>();

    /*
     * if we know features don't include the target group, no need
     * to inspect them for matches
     */
    if (positional && !positionalFeatureGroups.contains(group)
            || !positional && !nonPositionalFeatureGroups.contains(group))
    {
      return result;
    }

    if (positional)
    {
      addFeaturesForGroup(group, contactFeatureStarts, result);
      addFeaturesForGroup(group, features, result);
    }
    else
    {
      addFeaturesForGroup(group, nonPositionalFeatures, result);
    }
    return result;
  }

  /**
   * Answers the maximum score held for positional or non-positional features.
   * This may be Float.NaN if there are no features, are none has a non-NaN
   * score.
   * 
   * @param positional
   * @return
   */

  @Override
  public float getMaximumScore(boolean positional)
  {
    return positional ? positionalMaxScore : nonPositionalMaxScore;
  }

  /**
   * Answers the minimum score held for positional or non-positional features.
   * This may be Float.NaN if there are no features, are none has a non-NaN
   * score.
   * 
   * @param positional
   * @return
   */

  @Override
  public float getMinimumScore(boolean positional)
  {
    return positional ? positionalMinScore : nonPositionalMinScore;
  }

  @Override
  public List<SequenceFeature> getNonPositionalFeatures()
  {
    return getNonPositionalFeatures(new ArrayList<>());
  }

  /**
   * Answers a list of all non-positional features. If there are none, returns
   * an immutable empty list.
   * 
   * @return
   */

  @Override
  public List<SequenceFeature> getNonPositionalFeatures(
          List<SequenceFeature> result)
  {
    if (nonPositionalFeatures != null)
    {
      result.addAll(nonPositionalFeatures);
    }
    return result;
  }

  @Override
  public List<SequenceFeature> getPositionalFeatures()
  {
    return getPositionalFeatures(new ArrayList<>());
  }

  /**
   * Answers a list of all positional features stored, in no guaranteed order
   * 
   * @return
   */

  @Override
  public List<SequenceFeature> getPositionalFeatures(
          List<SequenceFeature> result)
  {

    /*
     * add any contact features - from the list by start position
     */
    if (contactFeatureStarts != null)
    {
      result.addAll(contactFeatureStarts);
    }

    /*
     * add any nested features
     */
    if (features != null)
    {
      result.addAll(features);
    }

    return result;
  }

  /**
   * Answers the total length of positional features (or zero if there are
   * none). Contact features contribute a value of 1 to the total.
   * 
   * @return
   */

  @Override
  public int getTotalFeatureLength()
  {
    return totalExtent;
  }

  /**
   * Answers true if this store has no features, else false
   * 
   * @return
   */

  @Override
  public boolean isEmpty()
  {
    boolean hasFeatures = (contactFeatureStarts != null
            && !contactFeatureStarts.isEmpty())
            || (nonPositionalFeatures != null
                    && !nonPositionalFeatures.isEmpty())
            || features.size() > 0;

    return !hasFeatures;
  }

  /**
   * Rescan all features to recompute any cached values after an entry has been
   * deleted. This is expected to be an infrequent event, so performance here is
   * not critical.
   */
  protected synchronized void rescanAfterDelete()
  {
    positionalFeatureGroups.clear();
    nonPositionalFeatureGroups.clear();
    totalExtent = 0;
    positionalMinScore = Float.NaN;
    positionalMaxScore = Float.NaN;
    nonPositionalMinScore = Float.NaN;
    nonPositionalMaxScore = Float.NaN;
    /*
     * scan non-positional features for groups and scores
     */
    if (nonPositionalFeatures != null)
    {
      List<SequenceFeature> list = nonPositionalFeatures;
      for (int i = 0, n = list.size(); i < n; i++)
      {
        SequenceFeature sf = list.get(i);
        nonPositionalFeatureGroups.add(sf.getFeatureGroup());
        float score = sf.getScore();
        nonPositionalMinScore = min(nonPositionalMinScore, score);
        nonPositionalMaxScore = max(nonPositionalMaxScore, score);
      }
    }

    /*
     * scan positional features for groups, scores and extents
     */

    rescanPositional(contactFeatureStarts);
    rescanPositional(features);
  }

  private void rescanPositional(Collection<SequenceFeature> sfs)
  {
    if (sfs == null)
    {
      return;
    }
    for (SequenceFeature sf : sfs)
    {
      positionalFeatureGroups.add(sf.getFeatureGroup());
      float score = sf.getScore();
      positionalMinScore = min(positionalMinScore, score);
      positionalMaxScore = max(positionalMaxScore, score);
      totalExtent += getFeatureLength(sf);
    }
  }

  /**
   * Adds the shift amount to the start and end of all positional features whose
   * start position is at or after fromPosition. Returns true if at least one
   * feature was shifted, else false.
   * 
   * @param fromPosition
   * @param shiftBy
   * @return
   */

  @Override
  public synchronized boolean shiftFeatures(int fromPosition, int shiftBy)
  {
    /*
     * Because begin and end are final fields (to ensure the data store's
     * integrity), we have to delete each feature and re-add it as amended.
     * (Although a simple shift of all values would preserve data integrity!)
     */
    boolean modified = false;
    List<SequenceFeature> list = getPositionalFeatures();
    for (int i = 0, n = list.size(); i < n; i++)
    {
      SequenceFeature sf = list.get(i);
      if (sf.getBegin() >= fromPosition)
      {
        modified = true;
        int newBegin = sf.getBegin() + shiftBy;
        int newEnd = sf.getEnd() + shiftBy;

        /*
         * sanity check: don't shift left of the first residue
         */
        if (newEnd > 0)
        {
          newBegin = Math.max(1, newBegin);
          SequenceFeature sf2 = new SequenceFeature(sf, newBegin, newEnd,
                  sf.getFeatureGroup(), sf.getScore());
          addFeature(sf2);
        }
        delete(sf);
      }
    }
    return modified;
  }

}