NWAligner.hh

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// vi: set ts=2 noet:
//
// (c) Copyright Rosetta Commons Member Institutions.
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/// @file NWAligner.hh
/// @brief class definition for a class that aligns two Sequence objects using a
/// the Needleman-Wunsch alignment algorithm.
/// @author James Thompson

#ifndef INCLUDED_core_sequence_NWAligner_hh
#define INCLUDED_core_sequence_NWAligner_hh

#include <core/types.hh>

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

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

namespace core {
namespace sequence {

class NWAligner : public Aligner {

public:

  /// @brief ctor
  NWAligner() {}

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

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

  static void init_matrix(
    Size y_len,
    Size x_len,
    ScoringSchemeOP ss,
    DP_Matrix & scores
  );

}; // class NWAligner

} // sequence
} // core

#endif