/*
 *                  Eoulsan development code
 *
 * This code may be freely distributed and modified under the
 * terms of the GNU Lesser General Public License version 2.1 or
 * later and CeCILL-C. This should be distributed with the code.
 * If you do not have a copy, see:
 *
 *      http://www.gnu.org/licenses/lgpl-2.1.txt
 *      http://www.cecill.info/licences/Licence_CeCILL-C_V1-en.txt
 *
 * Copyright for this code is held jointly by the Genomic platform
 * of the Institut de Biologie de l'École normale supérieure and
 * the individual authors. These should be listed in @author doc
 * comments.
 *
 * For more information on the Eoulsan project and its aims,
 * or to join the Eoulsan Google group, visit the home page
 * at:
 *
 *      http://outils.genomique.biologie.ens.fr/eoulsan
 *
 */

package fr.ens.biologie.genomique.eoulsan.bio.alignmentsfilters;

import htsjdk.samtools.SAMRecord;

import java.util.ArrayList;
import java.util.List;

/**
 * This class define a buffer that store all the alignments with the same read
 * name before to apply an alignment filter. This class only works with
 * alignment data where all the alignments for a read name are in straight.
 * @since 1.1
 * @author Laurent Jourdren
 * @author Claire Wallon
 */
public class ReadAlignmentsFilterBuffer {

  private final ReadAlignmentsFilter filter;
  private final List<SAMRecord> list = new ArrayList<>();
  private String currentName;
  private final boolean reuseResultList;

  /**
   * Add the provided alignment to a list of SAMRecord objects if this alignment
   * has the same read name as the other alignments of the list.
   * @param alignment SAM alignment
   * @return true if the alignment provides is stored, i.e. if it has the same
   *         read name as the other alignments already stored.
   */
  public boolean addAlignment(final SAMRecord alignment) {

    if (alignment == null) {
      return false;
    }

    final String name = parseAlignmentName(alignment);

    // The previous list of alignments has been already treated
    if (this.currentName == null) {
      this.currentName = name;
    }

    // The previous list of alignments is not already treated
    else {
      // The current alignment has a new read name
      if (!this.currentName.equals(name)) {
        this.currentName = null;
        return false;
      }
    }

    // The read name is equal to the previous
    // (so the alignment is in the same multiple alignment than the
    // previous one)
    this.list.add(alignment);
    return true;
  }

  /**
   * Get the list of the alignments that pass the tests of the filter with the
   * same read name. Warning if reuseResultList argument in the constructor is
   * set to true, this method will always returns the same object.
   * @return a list of SAM record
   */
  public List<SAMRecord> getFilteredAlignments() {

    // Filter alignment
    this.filter.filterReadAlignments(this.list);

    // Return the list of filtered alignment
    if (this.reuseResultList) {
      return this.list;
    }

    List<SAMRecord> results = new ArrayList<>(this.list);
    this.list.clear();
    this.currentName = null;

    return results;
  }

  /**
   * Parse alignment name.
   * @param alignment the alignment
   * @return the name of the sequence in the alignment
   */
  private static String parseAlignmentName(final SAMRecord alignment) {

    final String alignmentName = alignment.getReadName();
    final int spaceIndex = alignmentName.indexOf(' ');

    if (spaceIndex == -1) {
      return alignmentName;
    }

    return alignmentName.substring(0, spaceIndex);
  }

  //
  // Constructor
  //

  /**
   * Public constructor.
   * @param filter the filter to use with this buffer.
   */
  public ReadAlignmentsFilterBuffer(final ReadAlignmentsFilter filter) {

    this(filter, false);
  }

  /**
   * Public constructor.
   * @param filter the filter to use with this buffer
   * @param reuseResultList true if the getFilteredAlignments() method must
   *          return always the same internal list
   */
  public ReadAlignmentsFilterBuffer(final ReadAlignmentsFilter filter,
      final boolean reuseResultList) {

    if (filter == null) {
      throw new NullPointerException("The alignment filter is null");
    }

    this.filter = filter;
    this.reuseResultList = reuseResultList;
  }

}