#include <iostream>
#include <vector>
#include <fstream>
#include <string.h>
#include <limits>
#include <ctime>
#include <cstdlib>
#include <cstring>
#include <thread>
#include "FunzRand.h"
#include "GlobalVariables.h"
#include "GnuplotGlobal.h"
#include "MATLAB_Global.h"
#include "apngasm_Global.h"
#include "Q_tau_stat.h"
#include "E_Coli.h"
#include "ParameterEstimation_E_Coli.h"
#include "CV_rExp_tExp.h"
#include "Funz_C.h"
#include "Funz_C_Par.h"
#include "CV_rIG_tExp.h"
#include "CV_rExpIG_tExp.h"
#include "Molecular_rExp_tExp.h"
#include "Colori.h"
#include "Declar_funz.h"
#include "Funz_C_Inter.h"
#include "LoadBar.hpp"
#include "GlobalRandomVariables.h"
#include "ErrorsDefinition.h"
#include <sstream>
#include "mainFunctions.h"
#include <unistd.h>

Functions
int	createMakeFile ()

void	setDefoultGlobalVar ()

int	main (int argc, const char *argv[])

Variables
std::mutex	my_mutex

vector< double >	vettore_risposte

vector< std::string >	vettore_text

int	contatore_risposte = -1

int	automatic_ = 100

double	epsilon = 1.0

bool	multithread = false

bool	colors = true

int	n_thread_available = 1

string	fileEcoliRisp = "EcoliRisposte.Ecoli"

const string	nameLog = "LogEcoli.LogEcoli"

const string	EcoliPath = "EcoliPath.Ecoli"

unsigned int	seed_

unsigned int	seed_r

bool	same_seed = false

randomObj	rnd_ecoli
	this global variable is used to keep track of the seeds (random engine) More...

string	gnuplotOpen

string	gnuplotSetTerminalPlot

string	gnuplotSetTerminalSave_eps

string	gnuplotSetTerminalSave_png

std::string	firefox_path

std::string	gnuplotSetTerminalSave_gif

string	MATLAB_loc

string	MATLAB_call

string	apngas_lunch

string	apngas_opt

bool	no_apngams

const char *	homeDir = getenv ("HOME")

string	MainFolder

string	Location = homeDir

Function Documentation

int createMakeFile ( )

int main	(	int	argc,
		const char *	argv[]
	)

Main version 4.1.5. <- when change version and the file is no more compatible, change in function read_file_par() and save_risposte().

void setDefoultGlobalVar ( )

This function set the global variables to their default values ...

Variable Documentation

string apngas_lunch

Global Variable use to lunch apngas

string apngas_opt

Global Variable use to pass arguments to apngas (be careful it is different according to the system)

int automatic_ = 100

Variable to keep track of the MODE of simulation ... in otherwords, how to get the imput, from keybord and run the imput (0) from keybord and save the imput in std::vector<double> vettore_risposte; contatore_risposte keep track of the answer we read from the std::vector of answers (1) read from std::vector<double> vettore_risposte (2) automatic: 0 -> step by step version 1 -> setting parameters 2 -> running simulation

bool colors = true

int contatore_risposte = -1

const string EcoliPath = "EcoliPath.Ecoli"

double epsilon = 1.0

variable used to study the Diffusive limit

string fileEcoliRisp = "EcoliRisposte.Ecoli"

std::string firefox_path

string gnuplotOpen

string pass to system to open gnuplot

string gnuplotSetTerminalPlot

string pass to system to set terminal just to plot

string gnuplotSetTerminalSave_eps

string pass to system to set terminal to save .eps

std::string gnuplotSetTerminalSave_gif

string pass to system to set terminal to save .gif and create to movie

string gnuplotSetTerminalSave_png

string pass to system to set terminal to save .png and create to movie

const char* homeDir = getenv ("HOME")

string Location = homeDir

string MainFolder

string MATLAB_call

parameters to call MATLAB (i.e. -desktop ...)

string MATLAB_loc

location of MATLAB

bool multithread = false

std::mutex my_mutex

int n_thread_available = 1

const string nameLog = "LogEcoli.LogEcoli"

bool no_apngams

Global variable to use to set if we do not want to use apngasm

randomObj rnd_ecoli

this global variable is used to keep track of the seeds (random engine)

bool same_seed = false

unsigned int seed_

Variable used to reseed the random generator to allow the possibility to use the same random numbers in one Routine

unsigned int seed_r

vector<double> vettore_risposte

vector<std::string> vettore_text