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 
70 
73 
78 
83 
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 
BALL::NucleotideMapping::assignNaively
static NucleotideMapping assignNaively(Chain &a, Chain &b, unsigned int offset_a=0, unsigned int offset_b=0)
BALL_EXPORT
#define BALL_EXPORT
Definition: COMMON/global.h:50
BALL::NucleotideMapping::getSecondStrand
Chain * getSecondStrand() const
BALL::NucleotideMapping::assignFromAlignment
static NucleotideMapping assignFromAlignment(Chain &a, Chain &b, const Alignment &alignment)
BALL::Chain
Definition: chain.h:32
BALL::NucleotideMapping::secondToFirst
Residue * secondToFirst(Residue *b) const
BALL::NucleotideMapping::NucleotideMapping
NucleotideMapping()
hashMap.h
BALL::HashMap< Residue *, Residue * >
BALL::NucleotideMapping::getFirstStrand
Chain * getFirstStrand() const
BALL::Residue
Definition: residue.h:38
BALL::NucleotideMapping::firstToSecond
Residue * firstToSecond(Residue *a) const
BALL
Definition: constants.h:13
BALL::NucleotideMapping::Alignment
std::pair< const std::string, const std::string > Alignment
Definition: nucleotideMapping.h:24
BALL::NucleotideMapping::assignFromDistances
static NucleotideMapping assignFromDistances(Chain &a, Chain &b)
BALL::NucleotideMapping
Definition: nucleotideMapping.h:22