Aligner.hh

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// vi: set ts=2 noet:
//
// (c) Copyright Rosetta Commons Member Institutions.
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// (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
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/// @file Aligner.hh
/// @brief class definition for a class that aligns two Sequence objects using an
/// dynamic programming and an arbitrary scoring scheme.
/// @author James Thompson

#ifndef INCLUDED_core_sequence_Aligner_hh
#define INCLUDED_core_sequence_Aligner_hh

#include <core/types.hh>

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

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

#include <utility/pointer/ReferenceCount.hh>

#include <core/sequence/SequenceAlignment.fwd.hh>

namespace core {
namespace sequence {

class Aligner : public utility::pointer::ReferenceCount {

public:

  /// @brief ctor
  Aligner() {}

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

  virtual
  SequenceAlignment align(
    SequenceOP seq_y,
    SequenceOP seq_x,
    ScoringSchemeOP ss
  ) = 0;

  void validate_input(
    SequenceOP seq_y,
    SequenceOP seq_x,
    ScoringSchemeOP ss
  );

  SequenceAlignment traceback(
    SequenceOP seq_x,
    SequenceOP seq_y,
    DP_Matrix matrix,
    CellOP start
  );

}; // class Aligner

} // sequence
} // core

#endif