SecondaryStructure.h
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#ifndef SECONDARY_STRUCTURE_
#define SECONDARY_STRUCTURE_
#include "Motif.h"
#include "rna.h"
#include <iostream>
#include <string>
#include <vector>
using std::pair;
using std::string;
using std::vector;
class SecondaryStructure
{
public:
SecondaryStructure(void);
SecondaryStructure(const RNA& rna);
SecondaryStructure(bool empty);
void set_basepair(uint i, uint j);
void sort(void);
void insert_motif(const Motif& m);
double get_objective_score(int i) const;
void set_objective_score(int i, double s);
uint get_n_motifs(void) const;
uint get_n_bp(void) const;
void print(void) const;
string to_DBN() const;
string to_string() const;
vector<double> objective_scores_; // values of the different objective functions for that SecondaryStructure
vector<pair<uint, uint>> basepairs_; // values of the decision variable of the integer program
vector<Motif> motif_info_; // information about known motives in this secondary structure and their positions
size_t n_; // length of the RNA
size_t nBP_; // number of basepairs
RNA rna_; // RNA object which is folded
bool is_empty_structure; // Empty structure, returned when the solver does not find solutions anymore
};
// return if this SecondaryStructure s1 dominates s2
bool operator>(const SecondaryStructure& s1, const SecondaryStructure& s2);
bool operator>=(const SecondaryStructure& s1, const SecondaryStructure& s2);
// return if this SecondaryStructure s2 dominates s1
bool operator<(const SecondaryStructure& s1, const SecondaryStructure& s2);
bool operator<=(const SecondaryStructure& s1, const SecondaryStructure& s2);
// return wether SecondaryStructures are identical or not
bool operator==(const SecondaryStructure& s1, const SecondaryStructure& s2);
bool operator!=(const SecondaryStructure& s1, const SecondaryStructure& s2);
bool motif_sorter(Motif& m1, Motif& m2);
bool basepair_sorter(pair<uint, uint>& i, pair<uint, uint>& j);
inline double SecondaryStructure::get_objective_score(int i) const { return objective_scores_[i - 1]; }
inline void SecondaryStructure::set_objective_score(int i, double s) { objective_scores_[i - 1] = s; }
inline uint SecondaryStructure::get_n_motifs(void) const { return motif_info_.size(); }
inline uint SecondaryStructure::get_n_bp(void) const { return nBP_; }
#endif // SECONDARY_STRUCTURE_