@@ -83,9 +83,8 @@ int main(int argc, char* argv[])
("first-objective,c",po::value<unsignedint>(&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")orvm.count("-h")){
cout<<"Biorseo, bio-objective integer linear programming framework to predict RNA secondary "
...
...
@@ -132,8 +132,6 @@ int main(int argc, char* argv[])