NCBI C++ ToolKit
nuc_prop.hpp
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1 /* $Id: nuc_prop.hpp 33815 2007-05-04 17:18:18Z kazimird $
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31 
32 
33 #ifndef ALGO_SEQUENCE___NUC_PROP__HPP
34 #define ALGO_SEQUENCE___NUC_PROP__HPP
35 
36 #include <objmgr/seq_vector.hpp>
37 
40 
41 /// this class defines functions for calculating various
42 /// properties of nucleotide sequences
43 
45 {
46 public:
47  /// Tally the occurrences of each non-ambiguous n-mer.
48  static void CountNmers(CSeqVector& seqvec, int n, vector<int>& table);
49 
50  /// Encode an n-mer as an integer.
51  static int Nmer2Int(const char *seq, int n);
52 
53  /// Decode an integer representation of an n-mer.
54  static void Int2Nmer(int nmer_int, int nmer_size, string& out);
55 
56  /// The number of distinct n-mers (4^n)
57  static int NumberOfNmers(int n);
58 
59  /// Calculate percent G+C+S
60  static int GetPercentGC(const CSeqVector& seqvec);
61 
62 private:
63  static int Nuc2Nybble(char nuc);
64  static char Nybble2Nuc(int n);
65 };
66 
69 
70 #endif // ALGO_SEQUENCE___NUC_PROP__HPP
this class defines functions for calculating various properties of nucleotide sequences
Definition: nuc_prop.hpp:45
CSeqVector –.
Definition: seq_vector.hpp:65
std::ofstream out("events_result.xml")
main entry point for tests
#define END_NCBI_SCOPE
End previously defined NCBI scope.
Definition: ncbistl.hpp:103
#define END_SCOPE(ns)
End the previously defined scope.
Definition: ncbistl.hpp:75
#define BEGIN_NCBI_SCOPE
Define ncbi namespace.
Definition: ncbistl.hpp:100
#define BEGIN_SCOPE(ns)
Define a new scope.
Definition: ncbistl.hpp:72
#define NCBI_XALGOSEQ_EXPORT
Definition: ncbi_export.h:1017
<!DOCTYPE HTML >< html > n< header > n< title > PubSeq Gateway Help Page</title > n< style > n table
yy_size_t n
Modified on Sat May 25 14:20:24 2024 by modify_doxy.py rev. 669887