source: trunk/yat/utility/Alignment.h @ 873

#ifndef _theplu_yat_utility_alignment_
#define _theplu_yat_utility_alignment_

// $Id: Alignment.h 873 2007-09-18 01:14:38Z peter $

/*
  Copyright (C) 2004 Jari Häkkinen, Peter Johansson
  Copyright (C) 2005 Peter Johansson
  Copyright (C) 2006 Jari Häkkinen

  This file is part of the yat library, http://trac.thep.lu.se/trac/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 2 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 this program; if not, write to the Free Software
  Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA
  02111-1307, USA.
*/

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

namespace theplu {
namespace yat {
namespace utility {

  class matrix;

  ///
  /// Function performing alignment following the Needleman-Wunch
  /// algorithm. The algorithm starts from the dot-matrix, \a s, where
  /// \f$ s_{ij} \f$ describes how well element \f$ i \f$ in the first
  /// sequence match to element \f$ j \f$ in the second sequence. A
  /// path through this matrix corresponds to an alignment of the two
  /// sequences, in which a diagonal step over a matrix element
  /// corresponds to a match between the corresponding sequnce
  /// elements and a vertical or a horizontal step corresponds to
  /// inserting a gap in one of the sequnces. The function maximizes
  /// \f$ \sum s_{ij}-n \f$ \a gap, where the first sum goes over all
  /// matches and the second term is a penalty term for inserting \f$
  /// n \f$ gaps. Default is to have the \a gap cost set to zero. The
  /// vector \a path contains information about which elements that
  /// were matched. If the first element in the first sequence was
  /// matched to the first element in the second sequence, the last
  /// element in \a path is pair(0,0).
  ///
  /// @return the global maximum alignment score.
  ///
  double NeedlemanWunsch(const utility::matrix& s,
                         std::vector<std::pair<size_t, size_t> >& path,
                         const double gap);

  /**
     \brief Local alignment following the Smith-Waterman
     algorithm. 

     The original paper can be found here:
     http://gel.ym.edu.tw/~chc/AB_papers/03.pdf

     Instead of looking at each sequence in its entirety the S-W algorithm
     compares segemnt of all possible lengths (LOCAL alignment) and chooses
     whichever maximises the similarity measure.

     \param s score matrix in which element \f$(i,j)\f$ is the score between
     element \f$i\f$ in first sequence vs element \f$j\f$ in second sequence.
     \param gap cost for having a gap (insertion or deletion)
     \param open_gap cost for open up a gap in sequence, in other words, for a
     gap of length \f$l\f$ the total cost is \f$open_gap + l*gap\f$.
   */
  double SmithWaterman(const utility::matrix& s,
                       double gap, double open_gap);

  /**
     SSearch does a rigorous Smith-Waterman search for similarity between 
     sequnces. For long sequences this may be very expensive (both in time and
     space) and BLAST or FASTA is preferable.

     @return score
   */
  double ssearch(std::string first, std::string second, double gap, 
                 double open_gap);

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

#endif