NeedlemanWunsch.h

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// Copyright (c) 2002-present, OpenMS Inc. -- EKU Tuebingen, ETH Zurich, and FU Berlin
// SPDX-License-Identifier: BSD-3-Clause
//
// --------------------------------------------------------------------------
// $Maintainer: Nora Wild $
// $Authors: Nora Wild $
// --------------------------------------------------------------------------
 
#include <OpenMS/DATASTRUCTURES/String.h>
#include <OpenMS/OpenMSConfig.h>
 
#include <vector>
 
namespace OpenMS
{
  class OPENMS_DLLAPI NeedlemanWunsch
  {
 
  public:
 
    enum class ScoringMatrix
    {
      identity,
      PAM30MS,
      SIZE_OF_SCORINGMATRIX
    };
 
    NeedlemanWunsch(ScoringMatrix matrix, int penalty);
 
    NeedlemanWunsch() = default;
 
    ~NeedlemanWunsch()=default;
 
    static const std::vector<std::string> NamesOfScoringMatrices;
 
    int align(const String& seq1, const String& seq2);
 
    void setMatrix(const ScoringMatrix& matrix);
    void setMatrix(const std::string& matrix);
 
    void setPenalty(const int penalty);
 
    ScoringMatrix getMatrix() const;
 
    int getPenalty() const;
 
  private:
    int gap_penalty_ = 5; 
    ScoringMatrix my_matrix_ = ScoringMatrix::PAM30MS; 
    std::vector<int> first_row_{}; 
    std::vector<int> second_row_{};
  };
 
}