rk.h

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#include <vector>
#include <string>
#include "metabolicnetwork.h"

using namespace std;

#ifndef RK_H
#define RK_H

class RK {
        private:
                map<int,string> knock_reacs;  //indices of efms for the matrix in metab_network 
                string key;

                MetabolicNetwork *metab_network;
                vector<double> min_yields;

                vector<int> inactive_reacs;

                vector<long> uncollapsed_ineff_efm_indices, collapsed_ineff_efm_indices,uncollapsed_eff_efm_indices;
                int avg_path_length,max_path_length,min_path_length;
        public:
                RK();
                RK(const RK &rk);
                RK(map<int,string> knock_reacs, MetabolicNetwork *metab_network);

                int get_avg_path_length() { return this->avg_path_length;}
                int get_max_path_length() { return this->max_path_length;}
                int get_min_path_length() { return this->min_path_length;}
                string get_key() { return this->key;}
                map<int,string>& get_knock_reacs() { return this->knock_reacs;}         
                vector<long>& get_uncollapsed_ineff_efm_indices() { return this->uncollapsed_ineff_efm_indices; }
                vector<long>& get_uncollapsed_eff_efm_indices() { return this->uncollapsed_eff_efm_indices; }

                int add_reac(int reac,long &rank);

                int add_reac_direct(int reac,double &rank);
                int add_reacs(map<int,string> reacs);
                int test_reac(int reac,long &rank);
                int is_core_collapsed(int &cnt_not_collapsed);
                long test_knock_reacs2(map<int,string> knock_reacs, vector<double> &min_yields, long &num_eff_efm_rem, long &num_ineff_efm_rem);
                friend ostream& operator<<(ostream& out, const RK& rk);
                
};

int find_common_efm(vector<RK> rks, int &num_shared_efms);
#endif