CompassScoringScheme.hh

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// 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.
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/// @file CompassScoringScheme.hh
/// @brief class definition for a profile-profile scoring scheme for
/// comparing two sequence profiles using the Compass method, published
/// by Sadreyev and Grishin.
/// @author James Thompson

#ifndef INCLUDED_core_sequence_CompassScoringScheme_hh
#define INCLUDED_core_sequence_CompassScoringScheme_hh

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

namespace core {
namespace sequence {

class CompassScoringScheme : public ScoringScheme {
public:

  /// @brief ctor
  CompassScoringScheme(
    Real open   = -4,
    Real extend = -1
  )
  {
    gap_open  ( open );
    gap_extend( extend );
    type("Compass");
  }

  ScoringSchemeOP clone() const {
    return new CompassScoringScheme(
      gap_open(),
      gap_extend()
    );
  }

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

  virtual Real score( SequenceOP seq1, SequenceOP seq2, Size pos1, Size pos2 );
}; // class CompassScoringScheme

} // sequence
} // core

#endif