BALL  1.5.0
nucleotideMapping.h
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1 #ifndef BALL_STRUCTURE_NUCLEOTIDEMAPPING_H
2 #define BALL_STRUCTURE_NUCLEOTIDEMAPPING_H
3 
4 #include <string>
5 
7 
8 namespace BALL
9 {
10  class Chain;
11  class Residue;
12 
22  {
23  public:
24  typedef std::pair<const std::string, const std::string> Alignment;
25 
27 
30 
40  static NucleotideMapping assignNaively(Chain& a, Chain& b, unsigned int offset_a = 0, unsigned int offset_b = 0);
41 
50 
67  static NucleotideMapping assignFromAlignment(Chain& a, Chain& b, const Alignment& alignment);
68 
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93 
103 
105  private:
107  NucleotideMapping(Chain& a, Chain& b, const NucleotideMap& a_to_b, const NucleotideMap& b_to_a);
108 
109  Chain* a_;
110  Chain* b_;
111 
112  NucleotideMap a_to_b_;
113  NucleotideMap b_to_a_;
114  };
115 }
116 
117 #endif //BALL_STRUCTURE_NUCLEOTIDEMAPPING_H
118 
Definition: constants.h:13
Chain * getFirstStrand() const
static NucleotideMapping assignFromDistances(Chain &a, Chain &b)
static NucleotideMapping assignNaively(Chain &a, Chain &b, unsigned int offset_a=0, unsigned int offset_b=0)
static NucleotideMapping assignFromAlignment(Chain &a, Chain &b, const Alignment &alignment)
Residue * secondToFirst(Residue *b) const
std::pair< const std::string, const std::string > Alignment
Chain * getSecondStrand() const
Residue * firstToSecond(Residue *a) const
#define BALL_EXPORT
Definition: COMMON/global.h:50