NeedlemanWunsch.h

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// $Maintainer: Nora Wild $
// $Authors: Nora Wild $
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#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_{};
  };

}