MOIP.h
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#ifndef MOIP_H_
#define MOIP_H_
#define IL_STD
#include "SecondaryStructure.h"
#include "rna.h"
#include <ilcplex/ilocplex.h>
using std::vector;
const double PRECISION = 0.0001;
class MOIP
{
public:
static uint ncores;
typedef enum { MIN, MAX } DirType;
typedef enum { FR, LO, UP, DB, FX } BoundType;
MOIP(const RNA& rna, const vector<Motif>& motifSites);
~MOIP(void);
void solve_objective(int o, double min, double max);
uint get_n_solutions(void) const;
const SecondaryStructure& solution(uint i) const;
void extend_pareto(double lambdaMin, double lambdaMax);
bool allowed_basepair(size_t u, size_t v) const;
void add_solution(const SecondaryStructure& s);
private:
bool is_undominated_yet(const SecondaryStructure& s);
void add_problem_constraints(const IloModel& model_);
size_t get_yuv_index(size_t u, size_t v) const;
size_t get_Cpxi_index(size_t x_i, size_t i_on_j) const;
IloNumExprArg& y(size_t u, size_t v); // Direct reference to y^u_v in basepair_dv_
IloNumExprArg& C(size_t x, size_t i); // Direct reference to C_p^xi in insertion_dv_
RNA rna_; // RNA object
vector<Motif> insertion_sites_; // Potential Motif insertion sites
const float beta_; // beta parameter of the probability function
double lambdaMin_; // minimum threshold value for the probability value
double lambdaMax_; // maximum threshold value for the probability value
int vp_; // vp_ variable for penalization of the probability score
float theta_; // theta parameter for the probability function
IloEnv env_; // environment CPLEX object
IloNumVarArray basepair_dv_; // Decision variables
IloNumVarArray insertion_dv_; // Decision variables
vector<SecondaryStructure> pareto_; // Vector of results
vector<vector<size_t>> index_of_Cxip_; // Stores the indexes of the Cxip in insertion_dv_
vector<vector<size_t>> index_of_yuv_; // Stores the indexes of the y^u_v in basepair_dv_ in a complex way. Use get_yuv_index(u,v) to retrieve.
vector<size_t> index_of_first_components; // Stores the indexes of Cx1p in insertion_dv_
};
inline void MOIP::add_solution(const SecondaryStructure& s) { pareto_.push_back(s); }
inline uint MOIP::get_n_solutions(void) const { return pareto_.size(); }
inline const SecondaryStructure& MOIP::solution(uint i) const { return pareto_[i]; }
inline IloNumExprArg& MOIP::y(size_t u, size_t v) { return basepair_dv_[get_yuv_index(u, v)]; }
inline IloNumExprArg& MOIP::C(size_t x, size_t i) { return insertion_dv_[get_Cpxi_index(x, i)]; }
#endif // MOIP_H_