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ensemble_analyzer_main.cpp
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ensemble_analyzer_main.cpp
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#include <iostream>
#include "simulation.h"
#include <string.h>
using namespace std;
int main(int argc, char* argv[]) {
Simulation sim;
Rloop_equilibrium_model model;
bool sandbox = false;
//process command line arguments
sim.set_infile(argv[1]);
sim.set_outfile(argv[2]);
for (int i=3; i<argc; i++) {
if (!strcmp(argv[i], "--a")) {
model.seta(atof(argv[i+1]));
i++;
}
else if (!strcmp(argv[i], "--N")) {
if (!strcmp(argv[i+1],"auto")){
sim.set_auto_domain_size(true);
}
else{
model.setN(atoi(argv[i+1]));
}
i++;
}
else if (!strcmp(argv[i], "--sigma")) {
model.set_superhelicity(atof(argv[i+1]));
i++;
}
else if (!strcmp(argv[i], "--minlength")) {
sim.set_minlength(atoi(argv[i+1]));
i++;
}
else if (!strcmp(argv[i], "--reverse")) {
sim.reverse_input();
}
else if (!strcmp(argv[i], "--complement")) {
sim.complement_input();
}
else if (!strcmp(argv[i], "--invert")) {
sim.complement_input();
sim.reverse_input();
}
else if (!strcmp(argv[i], "--homopolymer")) {
model.set_bp_energy_override(atof(argv[i+1]));
i++;
}
//options specific to ensemble analyzer
else if (!strcmp(argv[i], "--sandbox")) {
sandbox = true;
}
else if (!strcmp(argv[i], "--bedfile")) {
sim.set_bedfile(true);
}
else if (!strcmp(argv[i], "--unconstrained")) {
model.set_unconstrained(true);
}
else if (!strcmp(argv[i], "--circular")) {
sim.set_circular();
}
else if (!strcmp(argv[i], "--residuals")) {
sim.set_residuals(true);
}
else if (!strcmp(argv[i], "--sensitivity")) {
sim.set_power_threshold(atoi(argv[i+1]));
i++;
}
else if (!strcmp(argv[i], "--top")) {
sim.set_top(atoi(argv[i+1]));
i++;
}
else if (!strcmp(argv[i], "--dump")) {
sim.set_dump(true);
}
else if (!strcmp(argv[i], "--localaverageenergy")) {
sim.set_average_g(true);
}
else{
cout << "Unrecognized command line option: " << argv[i] << endl;
exit(1);
}
}
sim.add_model(model);
if (sandbox){
sim.sandbox();
return 0;
}
sim.simulation_A();
return 0;
}