ScoringScheme.hh

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// vi: set ts=2 noet:
//
// (c) Copyright Rosetta Commons Member Institutions.
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/// @file ScoringScheme.hh
/// @brief abstract base class for representing scoring schemes for alignments.
/// @detailed ScoringScheme objects contain two scoring rules:
/// - a rule for comparing any character from a sequence to a gap character (usually
/// liste as gap insertion and gap extension, or d and e)
/// - a rule for scoring two elements from a sequence (simply S)
/// Generally the rule for scoring gaps is composed of a gap insertion and a gap
/// extension parameter. It's important to note that alignments derived using
/// the ScoringScheme and Aligner objects are only guaranteed to be optimal if
/// every element of S is bigger than -2 * e.
/// @author James Thompson

#ifndef INCLUDED_core_sequence_ScoringScheme_hh
#define INCLUDED_core_sequence_ScoringScheme_hh

// Unit headers
#include <core/sequence/ScoringScheme.fwd.hh>

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

// AUTO-REMOVED #include <utility/exit.hh>
#include <utility/io/izstream.fwd.hh>
#include <utility/file/FileName.fwd.hh>
#include <utility/pointer/ReferenceCount.hh>

#include <string>

namespace core {
namespace sequence {

class ScoringScheme : public utility::pointer::ReferenceCount {

public:

  /// @brief ctor
  ScoringScheme();

  /// @brief dtor
  virtual ~ScoringScheme();

  /// @brief clone method.
  virtual ScoringSchemeOP clone() const = 0;

  /// @brief Initialize from a file.
  virtual void read_from_file( utility::file::FileName const & /*fn*/ );

  virtual void read_data( utility::io::izstream & /*input*/ );

  /// @brief Gets the gap opening penalty.
  virtual Real gap_open() const;

  /// @brief Gets the gap extension penalty.
  virtual Real gap_extend() const;

  /// @brief Sets the gap opening penalty.
  void gap_open( Real const gap_open );

  /// @brief Sets the gap extension penalty.
  void gap_extend( Real const gap_extend );

  /// @brief getters for type, which is a unique string name for this object.
  std::string type() const;

  /// @brief getters for type, which is a unique string name for this object.
  void type( std::string new_type );

  virtual Real score(
    SequenceOP seq1,
    SequenceOP seq2,
    Size pos1,
    Size pos2
  ) = 0;

  /// @brief Utility method for producing useful error messages and exiting
  /// from program. Declared const which is funny, because exiting the program
  /// certainly changes the state of this object! This might be replaced with
  /// exception handling if we ever start using those.
  void unimplemented_method_error( std::string const & method_name ) const;

  bool is_good(
    Real const & num
  );

private:
  Real gap_open_;
  Real gap_extend_;
  std::string type_;
}; // class ScoringScheme

} // sequence
} // core

#endif