Aligner.h

#ifndef _theplu_yat_utility_aligner_
#define _theplu_yat_utility_aligner_

// $Id: Aligner.h 3114 2013-11-10 23:51:47Z peter $

/*
  Copyright (C) 2012 Peter Johansson
  Copyright (C) 2013 Jari Häkkinen, Peter Johansson

  This file is part of the yat library, http://dev.thep.lu.se/yat

  The yat library 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.

  The yat library 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 yat. If not, see <http://www.gnu.org/licenses/>.
*/

#include <cstddef>
#include <vector>

namespace theplu {
namespace yat {
namespace utility {

  class Matrix;

  class Aligner
  {
  public:
    enum direction { none, right, down, diagonal };

    Aligner(double gap=0, double open_gap=0);

    Aligner(double vertical_gap, double open_vertical_gap,
            double horizon_gap, double open_horizon_gap);

    double needleman_wunsch(const Matrix& d);

    double smith_waterman(const Matrix& d);

    void operator()(const Matrix& dot, Matrix& score);

    const direction& alignment(size_t i, size_t j) const;

  private:
    direction& cigar(size_t i, size_t j);

    size_t columns_;
    double vertical_gap_;
    double open_vertical_gap_;
    double horizon_gap_;
    double open_horizon_gap_;
    std::vector<direction> alignment_;
  };

}}} // of namespace utility, yat, and theplu

#endif