Alignment.h

#ifndef _theplu_yat_utility_alignment_
#define _theplu_yat_utility_alignment_

// $Id: Alignment.h 3210 2014-05-05 06:10:02Z peter $

/*
  Copyright (C) 2004 Jari Häkkinen, Peter Johansson
  Copyright (C) 2005 Peter Johansson
  Copyright (C) 2006 Jari Häkkinen
  Copyright (C) 2007, 2008 Jari Häkkinen, Peter Johansson
  Copyright (C) 2012, 2014 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 "deprecate.h"

#include <string>
#include <utility>
#include <vector>

namespace theplu {
namespace yat {
namespace utility {

  class Matrix;

  double NeedlemanWunsch(const utility::Matrix& s,
                         std::vector<std::pair<size_t, size_t> >& path,
                         const double gap);

  double SmithWaterman(const utility::Matrix& s,
                       double gap, double open_gap) YAT_DEPRECATE;

  double ssearch(std::string first, std::string second, double gap,
                 double open_gap, double mismatch=0.0);

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

#endif