OpenMS  3.0.0
NeedlemanWunsch.h
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34 
36 #include <OpenMS/OpenMSConfig.h>
37 
38 #include <vector>
39 
40 namespace OpenMS
41 {
46  class OPENMS_DLLAPI NeedlemanWunsch
47  {
48 
49  public:
50 
52  enum class ScoringMatrix
53  {
54  identity,
55  PAM30MS,
56  SIZE_OF_SCORINGMATRIX
57  };
58 
60  NeedlemanWunsch(ScoringMatrix matrix, int penalty);
61 
63  NeedlemanWunsch() = default;
64 
66  ~NeedlemanWunsch()=default;
67 
69  static const std::vector<std::string> NamesOfScoringMatrices;
70 
75  int align(const String& seq1, const String& seq2);
76 
81  void setMatrix(const ScoringMatrix& matrix);
82  void setMatrix(const std::string& matrix);
83 
85  void setPenalty(const int penalty);
86 
88  ScoringMatrix getMatrix() const;
89 
91  int getPenalty() const;
92 
93  private:
94  int gap_penalty_ = 5;
95  ScoringMatrix my_matrix_ = ScoringMatrix::PAM30MS;
96  std::vector<int> first_row_{};
97  std::vector<int> second_row_{};
98  };
99 
100 }
OpenMS::NeedlemanWunsch::ScoringMatrix
ScoringMatrix
contains the valid matrices and the number of them
Definition: NeedlemanWunsch.h:52
OpenMS::NeedlemanWunsch::NamesOfScoringMatrices
static const std::vector< std::string > NamesOfScoringMatrices
Names of valid matrices.
Definition: NeedlemanWunsch.h:69
OpenMS::String
A more convenient string class.
Definition: String.h:58
OpenMS
Main OpenMS namespace.
Definition: FeatureDeconvolution.h:47
OpenMS::NeedlemanWunsch
This class contains functions that are used to calculate the global alignment score of two amino acid...
Definition: NeedlemanWunsch.h:46
String.h