[jalview.git] / src / jalview / datamodel / features / FeatureStoreJS.java

/*
 * 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 java.util.ArrayList;
import java.util.List;

/**
 * An adaption of FeatureStore that is efficient and lightweight, accelerating
 * processing speed in JavaScript.
 * 
 * @author gmcarstairs
 * @author Bob Hanson 2019.08.03
 *
 */
public class FeatureStoreJS extends FeatureStore
{
  boolean contactsTainted = true;

  /**
   * internal reference to features as an ArrayList
   */
  private ArrayList<SequenceFeature> featureList;

  /**
   * Constructor
   */
  public FeatureStoreJS()
  {
    features = featureList = new ArrayList<>();
  }

  /**
   * 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
   */
  @Override
  protected synchronized boolean addContactFeature(SequenceFeature feature)
  {
    if (contactFeatureStarts == null)
    {
      contactFeatureStarts = new ArrayList<>();
      contactFeatureEnds = new ArrayList<>();
    }
    contactFeatureStarts.add(
            findFirstBegin(contactFeatureStarts, feature.begin), feature);
    contactFeatureEnds.add(findFirstEnd(contactFeatureEnds, feature.end),
            feature);
    return true;
  }

  /**
   * Adds one feature to the IntervalStore that can manage nested features
   * (creating the IntervalStore if necessary)
   */
  @Override
  protected synchronized void addNestedFeature(SequenceFeature feature)
  {
    featureList.add(findFirstBegin(featureList, feature.begin), feature);
  }

  /**
   * Returns a (possibly empty) list of features whose extent overlaps the given
   * range. The returned list is not ordered. Contact features are included if
   * either of the contact points lies within the range.
   * 
   * @param start
   *          start position of overlap range (inclusive)
   * @param end
   *          end position of overlap range (inclusive)
   * @return
   */

  @Override
  public List<SequenceFeature> findOverlappingFeatures(long start, long end,
          List<SequenceFeature> result)
  {
    if (result == null)
    {
      result = new ArrayList<>();
    }
    if (contactFeatureStarts != null)
    {
      if (start == end)
      {
        findContactPoints(contactFeatureStarts, start, result, true);
        findContactPoints(contactFeatureEnds, start, result, false);
      }
      else
      {
        findContactFeatures(start, end, result);
      }
    }
    if (featureList.size() > 0)
    {
      findOverlaps(start, end, result);
    }
    return result;
  }

  // The following methods use a linked list of containment in SequenceFeature
  // rather than IntervalStore.
  //
  // There are two parts --- initialization, and overlap searching.
  //
  // Initialization involves two steps:
  //
  // (1) sorting of features by start position using a standard Array.sort with
  // Comparator.
  // (2) linking of features, effectively nesting them.
  //
  // Searching involves three steps:
  //
  // (1) binary search for a starting point within the sorted features array.
  // (2) traverse the linked lists with an end check to read out the
  // overlapped features at this position.
  // (3) For an interval, find the last feature that starts in this interval,
  // and add all features up through that feature.
  //
  // All of this is done with very simple standard methods.

  // Initialization

  /*
   * contact features ordered by first contact position
   */
  private SequenceFeature[] orderedFeatureStarts;

  private void rebuildArrays(int n)
  {
    // Arrays.sort(orderedFeatureStarts, startComp);
    orderedFeatureStarts = featureList
            .toArray(new SequenceFeature[featureList.size()]);
    linkFeatures(orderedFeatureStarts);
  }

  // /**
  // * just a standard Comparator
  // */
  // private static StartComparator startComp;
  //
  // class StartComparator implements Comparator<SequenceFeature>
  // {
  //
  // @Override
  // public int compare(SequenceFeature o1, SequenceFeature o2)
  // {
  // int p1 = o1.begin;
  // int p2 = o2.begin;
  // return (p1 < p2 ? -1 : p1 > p2 ? 1 : 0);
  // }
  //
  // }

  /**
   * Run through the sorted sequence array once, building the containedBy linked
   * list references. Does a check first to make sure there is actually
   * something out there that is overlapping. A null for sf.containedBy means
   * there are no overlaps for this feature.
   * 
   * @param intervals
   */
  private void linkFeatures(SequenceFeature[] intervals)
  {
    if (intervals.length < 2)
    {
      return;
    }
    int maxEnd = intervals[0].end;
    for (int i = 1, n = intervals.length; i < n; i++)
    {
      SequenceFeature sf = intervals[i];
      if (sf.begin <= maxEnd)
      {
        sf.containedBy = getContainedBy(intervals[i - 1], sf);
      }
      if (sf.end > maxEnd)
      {
        maxEnd = sf.end;
      }
    }
  }

  /**
   * Since we are traversing the sorted feature array in a forward direction,
   * all elements prior to the one we are working on have been fully linked. All
   * we are doing is following those links until we find the first array feature
   * with a containedBy element that has an end &gt;= our begin point. It is
   * generally a very short list -- maybe one or two depths. But it might be
   * more than that.
   * 
   * @param sf
   * @param sf0
   * @return
   */
  private SequenceFeature getContainedBy(SequenceFeature sf,
          SequenceFeature sf0)
  {
    int begin = sf0.begin;
    while (sf != null)
    {
      if (begin <= sf.end)
      {
        // System.out.println("\nFS found " + sf0.index + ":" + sf0
        // + "\nFS in " + sf.index + ":" + sf);
        return sf;
      }
      sf = sf.containedBy;
    }
    return null;
  }

  // search-stage methods

  /**
   * Binary search for contact start or end at a given (Overview) position.
   * 
   * @param l
   * @param pos
   * @param result
   * @param isStart
   * 
   * @author Bob Hanson 2019.07.30
   */
  private static void findContactPoints(List<SequenceFeature> l, long pos,
          List<SequenceFeature> result, boolean isStart)
  {
    int low = 0;
    int high = l.size() - 1;
    while (low <= high)
    {
      int mid = (low + high) >>> 1;
      SequenceFeature f = l.get(mid);
      switch (Long.signum((isStart ? f.begin : f.end) - pos))
      {
      case -1:
        low = mid + 1;
        continue;
      case 1:
        high = mid - 1;
        continue;
      case 0:
        int m = mid;
        result.add(f);
        // could be "5" in 12345556788 ?
        while (++mid <= high && (f = l.get(mid)) != null
                && (isStart ? f.begin : f.end) == pos)
        {
          result.add(f);
        }
        while (--m >= low && (f = l.get(m)) != null
                && (isStart ? f.begin : f.end) == pos)
        {
          result.add(f);
        }
        return;
      }
    }
  }

  /**
   * Find all overlaps; special case when there is only one feature. The
   * required array of start-sorted SequenceFeature is created lazily.
   * 
   * @param start
   * @param end
   * @param result
   */
  private void findOverlaps(long start, long end,
          List<SequenceFeature> result)
  {
    int n = featureList.size();
    switch (n)
    {
    case 0:
      return;
    case 1:
      checkOne(featureList.get(0), start, end,
              result);
      return;
    default:
      if (orderedFeatureStarts == null)
      {
        rebuildArrays(n);
      }
      break;
    }

    // (1) Find the closest feature to this position.

    int index = findClosestFeature(orderedFeatureStarts, start);
    SequenceFeature sf = (index < 0 ? null : orderedFeatureStarts[index]);

    // (2) Traverse the containedBy field, checking for overlap.

    while (sf != null)
    {
      if (sf.end >= start)
      {
        result.add(sf);
      }
      sf = sf.containedBy;
    }

    // (3) For an interval, find the last feature that starts in this interval,
    // and add all features up through that feature.

    if (end > start)
    {
      // fill in with all features that start within this interval, fully
      // inclusive
      int index2 = findClosestFeature(orderedFeatureStarts, end);
      while (++index <= index2)
      {
        result.add(orderedFeatureStarts[index]);
      }

    }
  }

  /**
   * Quick check when we only have one feature.
   * 
   * @param sf
   * @param start
   * @param end
   * @param result
   */
  private void checkOne(SequenceFeature sf, long start, long end,
          List<SequenceFeature> result)
  {
    if (sf.begin <= end && sf.end >= start)
    {
      result.add(sf);
    }
    return;
  }

  @Override
  protected boolean containsFeature(SequenceFeature feature)
  {

    int pos = findFirstBegin(featureList,
            feature.begin);
    int len = featureList.size();
    while (pos < len)
    {
      SequenceFeature sf = featureList.get(pos);
      if (sf.begin > feature.begin)
      {
        return false; // no match found
      }
      if (sf.equals(feature))
      {
        return true;
      }
      pos++;
    }
    return false;

  }

  /**
   * A binary search identical to the one used for contact start/end, but here
   * we return the feature itself. Unlike Collection.BinarySearch, all we have
   * to be is close, not exact, and we make sure if there is a string of
   * identical starts, then we slide to the end so that we can check all of
   * them.
   * 
   * @param l
   * @param pos
   * @return
   */
  private int findClosestFeature(SequenceFeature[] l, long pos)
  {
    int low = 0;
    int high = l.length - 1;
    while (low <= high)
    {
      int mid = (low + high) >>> 1;
      SequenceFeature f = l[mid];
      switch (Long.signum(f.begin - pos))
      {
      case -1:
        low = mid + 1;
        continue;
      case 1:
        high = mid - 1;
        continue;
      case 0:

        while (++mid <= high && l[mid].begin == pos)
        {
          ;
        }
        return --mid;
      }
    }
    return (high < 0 ? -1 : high);
  }

  /**
   * Adds contact features to the result list where either the second or the
   * first contact position lies within the target range
   * 
   * @param from
   * @param to
   * @param result
   */
  @Override
  protected void findContactFeatures(long from, long to,
          List<SequenceFeature> result)
  {
    findContactStartOverlaps(from, to, result);
    findContactEndOverlaps(from, to, result);
  }

  /**
   * Adds to the result list any contact features whose end (second contact
   * point), but not start (first contact point), lies in the query from-to
   * range
   * 
   * @param from
   * @param to
   * @param result
   */

  private void findContactEndOverlaps(long from, long to,
          List<SequenceFeature> result)
  {
    // find the first contact feature (if any)
    // with end point not before the target range

    for (int i = findFirstEnd(contactFeatureEnds,
            from), n = contactFeatureEnds.size(); i < n; i++)
    {
      SequenceFeature sf = contactFeatureEnds.get(i);
      if (sf.begin >= from && sf.begin <= to)
      {
        // this feature's first contact position lies in the search range
        // so we don't include it in results a second time
        continue;
      }

      if (sf.end > to)
      {
        // this feature (and all following) has end point after the target range
        break;
      }

      // feature has end >= from and end <= to
      // i.e. contact end point lies within overlap search range
      result.add(sf);
    }
  }

  /**
   * Adds contact features whose start position lies in the from-to range to the
   * result list
   * 
   * @param from
   * @param to
   * @param result
   */

  private void findContactStartOverlaps(long from, long to,
          List<SequenceFeature> result)
  {
    for (int i = findFirstBegin(contactFeatureStarts,
            from), n = contactFeatureStarts.size(); i < n; i++)
    {
      SequenceFeature sf = contactFeatureStarts.get(i);
      if (sf.begin > to)
      {
        break;
      }
      result.add(sf);
    }
  }

  @Override
  protected int findFirstBegin(List<SequenceFeature> list, long pos)
  {
    int start = 0;
    int end = list.size() - 1;
    int matched = list.size();

    while (start <= end)
    {
      int mid = (start + end) / 2;
      if (list.get(mid).begin >= pos)
      {
        matched = mid;
        end = mid - 1;
      }
      else
      {
        start = mid + 1;
      }
    }
    return matched;
  }

  @Override
  protected int findFirstEnd(List<SequenceFeature> list, long pos)
  {
    int start = 0;
    int end = list.size() - 1;
    int matched = list.size();

    while (start <= end)
    {
      int mid = (start + end) / 2;
      if (list.get(mid).end >= pos)
      {
        matched = mid;
        end = mid - 1;
      }
      else
      {
        start = mid + 1;
      }
    }
    return matched;
  }


}