CompositeScoringScheme.hh

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// vi: set ts=2 noet:
//
// (c) Copyright Rosetta Commons Member Institutions.
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/// @file CompositeScoringScheme.hh
/// @brief class definition for a given scoring scheme for an alignment.
/// @detailed Scoring scheme based on comparing sequence columns based on
/// the additive combination of several ScoringScheme objects.
/// @author James Thompson

#ifndef INCLUDED_core_sequence_CompositeScoringScheme_hh
#define INCLUDED_core_sequence_CompositeScoringScheme_hh

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

#include <utility/vector1_bool.hh>

namespace core {
namespace sequence {

class CompositeScoringScheme : public ScoringScheme {

public:
  CompositeScoringScheme() {
    gap_open  ( -4 );
    gap_extend( -1 );
    type("Composite");
  }

  /// @brief ctor
  CompositeScoringScheme(
    Real gap_open_in,
    Real gap_extend_in,
    utility::vector1< ScoringSchemeOP > schemes
  ) :
    scoring_schemes_( schemes )
  {
    gap_open( gap_open_in );
    gap_extend( gap_extend_in );
    type("Composite");
  }

  ScoringSchemeOP clone() const {
    // maybe clone the scoring_schemes() if object re-use ever causes a weird
    // problem.
    return new CompositeScoringScheme(
      gap_open(),
      gap_extend(),
      scoring_schemes()
    );
  }

  utility::vector1< ScoringSchemeOP > scoring_schemes() const {
    return scoring_schemes_;
  }

  Size count() const {
    return scoring_schemes_.size();
  }

  void add_scoring_scheme( ScoringSchemeOP scheme );

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

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

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

private:
  utility::vector1< ScoringSchemeOP > scoring_schemes_;
}; // class CompositeScoringScheme

} // sequence
} // core

#endif