Louis BECQUEY

solved wrong function selection

......@@ -60,7 +60,7 @@ int main(int argc, char* argv[])
string inputName, outputName, motifs_path_name, basename;
bool verbose = false;
float theta_p_threshold;
int obj_function_nbr, mychar;
char obj_function_nbr;
char mea_or_mfe = 'b'; // a for MFE, b for MEA
list<Fasta> f;
ofstream outfile;
......@@ -83,9 +83,8 @@ int main(int argc, char* argv[])
("first-objective,c", po::value<unsigned int>(&MOIP::obj_to_solve_)->default_value(2), "Objective to solve in the mono-objective portions of the algorithm")
("output,o", po::value<string>(&outputName), "A file to summarize the computation results")
("theta,t", po::value<float>(&theta_p_threshold)->default_value(1e-3, "0.001"), "Pairing probability threshold to consider or not the possibility of pairing")
("function,f", po::value<int>(&obj_function_nbr)->default_value('B'), "What objective function to use to include motifs: square of motif size in nucleotides like "
("function,f", po::value<char>(&obj_function_nbr)->default_value('B'), "What objective function to use to include motifs: square of motif size in nucleotides like "
"RNA-MoIP (A), light motif size + high number of components (B), site score (C), light motif size + site score + high number of components (D)")
("plop,p", po::value<int>(&mychar), "Just a test")
("mfe,E", "Minimize stacking energies as second criteria (should lead to MFE structure)")
("mea,A", "(default) Maximize expected accuracy as second criteria (should lead to MEA structure)")
......@@ -99,6 +98,7 @@ int main(int argc, char* argv[])
try {
po::store(po::parse_command_line(argc, argv, desc), vm); // can throw
po::notify(vm);
if (vm.count("help") or vm.count("-h")) {
cout << "Biorseo, bio-objective integer linear programming framework to predict RNA secondary "
......@@ -132,8 +132,6 @@ int main(int argc, char* argv[])
"--help for more information."
<< endl;
return EXIT_FAILURE;
} else {
cout << "char: " << char(obj_function_nbr) << " defaulted: " << vm["function"].defaulted() << " plop: " << vm.count("plop") << " " << char(mychar) << endl;
}
po::notify(vm); // throws on error, so do after help in case there are any problems
......@@ -182,8 +180,6 @@ int main(int argc, char* argv[])
else
cerr << "ERR: no source of modules provided !" << endl;
return 0;
MOIP myMOIP = MOIP(myRNA, source, motifs_path_name.c_str(), theta_p_threshold, verbose);
double min, max;
IloConstraintArray F(myMOIP.get_env());
......