SimpleScoringScheme.hh

Go to the documentation of this file.

// -*- mode:c++;tab-width:2;indent-tabs-mode:t;show-trailing-whitespace:t;rm-trailing-spaces:t -*-
// vi: set ts=2 noet:
//
// (c) Copyright Rosetta Commons Member Institutions.
// (c) This file is part of the Rosetta software suite and is made available under license.
// (c) The Rosetta software is developed by the contributing members of the Rosetta Commons.
// (c) For more information, see http://www.rosettacommons.org. Questions about this can be
// (c) addressed to University of Washington UW TechTransfer, email: license@u.washington.edu.

/// @file SimpleScoringScheme.hh
/// @brief class definition for a given scoring scheme for an alignment.
/// @detailed Scoring scheme based on comparing single characters from two sequences
/// with three types of score:
/// - score for a match (characters are equal)
/// - score for a mismatch (characters are not equal)
/// - affine gap penalties of the form penalty = A + Bk
/// @author James Thompson

#ifndef INCLUDED_core_sequence_SimpleScoringScheme_hh
#define INCLUDED_core_sequence_SimpleScoringScheme_hh

#include <core/types.hh>
// AUTO-REMOVED #include <core/sequence/Sequence.hh>
#include <core/sequence/Sequence.fwd.hh>
#include <core/sequence/ScoringScheme.hh>

#include <utility/file/FileName.fwd.hh>

namespace core {
namespace sequence {

class SimpleScoringScheme : public ScoringScheme {

public:

  /// @brief ctor
  SimpleScoringScheme(
    Real match_score    =  4,
    Real mismatch_score =  1,
    Real gap_open_in    = -4,
    Real gap_extend_in  = -1
  ) :
    match_score_( match_score ),
    mismatch_score_( mismatch_score )
  {
    gap_open( gap_open_in );
    gap_extend( gap_extend_in );
    type("Simple");
  }

  ScoringSchemeOP clone() const {
    return new SimpleScoringScheme(
      match_score(),
      mismatch_score(),
      gap_open(),
      gap_extend()
    );
  }

  /// @brief dtor
  virtual ~SimpleScoringScheme() {}

  virtual void read_from_file( utility::file::FileName const & fn );

  Real match_score() const;

  Real mismatch_score() const;

  virtual Real score( SequenceOP seq1, SequenceOP seq2, core::Size pos1, core::Size pos2 );

private:
  Real match_score_;
  Real mismatch_score_;
}; // class SimpleScoringScheme

} // sequence
} // core

#endif