MOIP.h
5.24 KB
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
#ifndef MOIP_H_
#define MOIP_H_
#define IL_STD
#include "SecondaryStructure.h"
#include "rna.h"
#include <ilconcert/ilomodel.h>
#include <ilcplex/ilocplex.h>
#include <iostream>
#include <vector>
using std::vector;
typedef struct argsf_ {
path motif_file;
std::mutex& posInsertionSites_mutex;
argsf_(path motif_file_, mutex& mutex_)
: motif_file(motif_file_), posInsertionSites_mutex(mutex_) {}
} file_and_mutex;
typedef struct argsm_ {
json_elem motif;
std::mutex& posInsertionSites_mutex;
argsm_(json_elem& motif_, mutex& mutex_)
: motif(motif_), posInsertionSites_mutex(mutex_) {}
} motif_and_mutex;
class MOIP
{
public:
MOIP(void);
MOIP(const RNA& rna, string source, string source_path, float theta, bool verbose);
~MOIP(void);
SecondaryStructure solve_objective(int o, double min, double max);
SecondaryStructure solve_objective(int o);
uint get_n_candidates(void) const;
uint get_n_solutions(void) const;
const SecondaryStructure& solution(uint i) const;
void search_between(double lambdaMin, double lambdaMax);
bool allowed_basepair(size_t u, size_t v) const;
void add_solution(const SecondaryStructure& s);
void remove_solution(uint i);
void forbid_solutions_between(double min, double max);
IloEnv& get_env(void);
static char obj_function_nbr_; // On what criteria do you want to insert motifs ?
static char obj_function2_nbr_; // Do you want to use MEA or MFE to determine the best energy score ?
static uint obj_to_solve_; // What objective do you prefer to solve in mono-objective portions of the algorithm ?
static double precision_; // decimals to keep in objective values, to avoid numerical issues. otherwise, solution with objective 5.0000000009 dominates solution with 5.0 =(
static bool allow_pk_; // Wether we forbid pseudoknots (false) or allow them (true)
static uint max_sol_nbr_; // Number of solutions to accept in the Pareto set before we give up the computation
private:
bool is_undominated_yet(const SecondaryStructure& s);
void define_problem_constraints(string& source);
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;
size_t get_xij_index(size_t u, size_t v) 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_
IloNumExprArg& x(size_t u, size_t v); // Direct reference to x_i,j in stacks_dv_
bool exists_vertical_outdated_labels(const SecondaryStructure& s) const;
bool exists_horizontal_outdated_labels(const SecondaryStructure& s) const;
void allowed_motifs_from_desc(file_and_mutex arg_struct);
void allowed_motifs_from_rin(file_and_mutex arg_struct);
void allowed_motifs_from_json(motif_and_mutex arg_struct);
bool verbose_; // Should we print things ?
// Elements of the problem
RNA rna_; // RNA object
vector<Motif> insertion_sites_; // Potential Motif insertion sites
vector<SecondaryStructure> pareto_; // Vector of results
// CPLEX objects
IloEnv env_; // environment CPLEX object
IloNumVarArray basepair_dv_; // Decision variables
IloNumVarArray insertion_dv_; // Decision variables
IloNumVarArray stacks_dv_; // Decision variables
IloModel model_; // Solver for objective 1
IloExpr obj1; // Objective function that counts inserted motifs
IloExpr obj2; // Objective function of expected accuracy
vector<vector<size_t>> index_of_Cxip_; // Stores the indexes of the Cxip in insertion_dv_
vector<size_t> index_of_first_components; // Stores the indexes of Cx1p in insertion_dv_
vector<vector<size_t>> index_of_yuv_; // Stores the indexes of the y^u_v in basepair_dv_
vector<vector<size_t>> index_of_xij_; //Stores the indexes of the xij variables (BioKop) in stacks_dv_
};
inline uint MOIP::get_n_solutions(void) const { return pareto_.size(); }
inline uint MOIP::get_n_candidates(void) const { return insertion_sites_.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)]; }
inline IloNumExprArg& MOIP::x(size_t u, size_t v) { return stacks_dv_[get_xij_index(u, v)]; }
inline SecondaryStructure MOIP::solve_objective(int o) { return solve_objective(o, 0, rna_.get_RNA_length()); }
inline IloEnv& MOIP::get_env(void) { return env_; }
#endif // MOIP_H_