options.h

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#include <vector>
#include <string>
#include "util.h"
using namespace std;

#ifndef OPTIONS_H
#define OPTIONS_H

/*
   Class: Options
   Contains options that are parsed from command line and printed to screen and output result file
*/

class Options {

        private:
                string config_fname;    
                string efm_bit_fname;
                string efm_meta_fname;
                string output_fname;
                string yields_fname;
                vector<string> init_knock_reacs;
                vector<string> target_reacs;
                vector<string> substrate_reacs;
                vector<string> transport_reacs;
                vector<double> min_yields;
                vector<double> min_core_yields;
                string use_xchg_reacs;          
                int max_efm_cands,max_rk_cands, max_reac_subset_length;
                string algorithm;
                string network_capacity;
        public:
                Options() {}
                Options(string config_fname);
        void    load(string config_fname);              
        void    print();
        void    print_to_file(ostream &out);

        int     get_max_rk_cands() { return this->max_rk_cands;}
        int     get_max_efm_cands() { return this->max_efm_cands;}
        int     get_max_reac_subset_length() { return this->max_reac_subset_length;}

        string  get_algorithm() { return this->algorithm;}
        string  get_network_capacity() { return this->network_capacity;}

        string  get_efm_bit_fname() { return this->efm_bit_fname;}
        string  get_efm_meta_fname() { return this->efm_meta_fname;}
        string  get_output_fname() { return this->output_fname;}
        string  get_yields_fname() { return this->yields_fname;}
        string  get_config_fname() { return this->config_fname;}

        string  get_use_xchg_reacs() { return this->use_xchg_reacs;}

        vector<string>& get_init_knock_reacs() { return this->init_knock_reacs;}
        vector<string>& get_target_reacs() {return this->target_reacs;}
        vector<string>& get_substrate_reacs() {return this->substrate_reacs;}
        vector<string>& get_transport_reacs() {return this->transport_reacs;}
        vector<double>& get_min_yields() { return this->min_yields;}
        vector<double>& get_min_core_yields(){ return this->min_core_yields;}

        //friend ostream& operator<<(ostream& out, const Options& opt);         
        void load_efm_meta_file(vector< vector<double> > &stoich, vector<string> &reacs_names, t_UnsignedInt &num_ems);
                
};
void parse_string( const string& str, const char separator, vector<string>& result );
#endif