MCAligner.hh

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// vi: set ts=2 noet:
//
// (c) Copyright Rosetta Commons Member Institutions.
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/// @file MCAligner.hh
/// @brief class definition for a class that aligns two Sequence objects using a
/// the Needleman-Wunsch alignment algorithm.
/// @author James Thompson

#ifndef INCLUDED_core_sequence_MCAligner_hh
#define INCLUDED_core_sequence_MCAligner_hh

#include <core/types.hh>

#include <core/sequence/Aligner.hh>
#include <core/sequence/Sequence.fwd.hh>
#include <core/sequence/ScoringScheme.fwd.hh>
#include <core/sequence/SequenceAlignment.fwd.hh>

namespace core {
namespace sequence {

class MCAligner : public Aligner {

public:

  /// @brief constructors
  MCAligner()          : kT_( 1 ) {}
  MCAligner( Real kT ) : kT_( kT ) {}

  /// @brief destructor
  virtual ~MCAligner() {}

  /// @brief Sets the kT used in the align method. A optimal value of kT means
  /// acceptance of less optimal decisions along the dynamic programming matrix.
  void kT( Real new_kT ) {
    kT_ = new_kT;
  }

  /// @brief Returns the kT used in the align method.
  Real kT() const {
    return kT_;
  }

  /// @brief Align these two Sequences using the given ScoringScheme. Rather
  /// than finding an optimal alignment, MCAligner uses a stochastic algorithm
  /// to generate an alignment at a given kT.
  /// @detailed The Needleman-Wunsch algorithm uses dynamic programming to
  /// generate an optimal alignment between two scoring sequences under a given
  /// scoring scheme.  Rather than making the best decision at each element of
  /// the dynamic programming matrix, MCAligner makes a stochastic decision
  /// between introducing a gap in seq_y, introducing a gap in seq_x, or aligning two
  /// characters between the two sequences. The decision is made by transforming the
  /// scores for each of the three possible decisions into probabilities using
  /// Boltzmann weighting of the scores for each possibility at a given kT. The kT
  /// is stored as a member variable of the MCAligner class, and accessor methods
  /// are provided above.

  virtual
  SequenceAlignment align(
    SequenceOP seq_y,
    SequenceOP seq_x,
    ScoringSchemeOP ss
  );

private:
  Real kT_;
}; // class MCAligner

} // sequence
} // core

#endif