main.cpp

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#include <iostream>
#include <fstream>   // file I/O
#include <getopt.h>
#include <string.h>
#include <time.h>
#include <iomanip>
#include <assert.h>
#ifdef PARALLEL
        #include <mpi.h>
#endif

using namespace std;

//#include "knocktest.h"
//#include "cpptest-htmloutput.h"
#include "general_hash_functions.h"
#include "ufes.h"
#include "enumeffknocks.h"
#include "options.h"
#include "util.h"
#include "bitefm.h"

int main(int argc, char** argv) {
        

        int c,init_only=0;
        //string efm_fname,reac_fname,substrate_fname,target_fname, init_knocks_fname,yield_fname, coreefm_fname;
        
        int nump=1, proc_id=0;
        string ko_fname,config_fname;

        #ifdef PARALLEL
        MPI_Init(&argc,&argv);
        util::get_proc_id_nump(proc_id,nump);
        #endif
                


        Options options;

        config_fname="configs.knock";
        while ((c = getopt(argc, argv, "c:y:")) >= 0) {
                switch (c) {
                        case 'c':  //efm file name
                                config_fname=optarg;
                                break;
                        case 'y': 
                                init_only=1;
                                break;
                }
        }       
        
        options.load(config_fname);
        if (proc_id==0)
                options.print();


        if (init_only && proc_id==0) 
                cout << endl << "\t"<<util::get_time_str()<<": loading and initializing network only."<<endl;

        MetabolicNetwork metab_network(options);

        if (init_only) {
                if (proc_id==0)
                        cout << endl << "\t"<<util::get_time_str()<<": network loaded and initialized only."<<endl;
                #ifdef PARALLEL         
                MPI_Finalize(); 
                #endif
                return 0;
        }



        ko_fname=options.get_output_fname();
        long ts = time (NULL);
        ko_fname=ko_fname+".";
        stringstream oss;
        oss << ts;
        ko_fname=ko_fname+oss.str();
        //add timestamp to ko_fname

        if (util::trim(ko_fname)=="") {
                if (proc_id==0)
                        cout << endl << "\t"<<util::get_time_str()<<": Output file name not given."<<endl;

        }

        if (nump>1) {
                stringstream proc_id_str;
                proc_id_str << "."<<proc_id;
                ko_fname=ko_fname+proc_id_str.str();
        }

        if (proc_id==0) {
                cout << endl << "\t"<<util::get_time_str()<<": metabolic network loaded..." <<endl;
                cout << endl << "\t"<<util::get_time_str();
        }


        EnumEffKnocks enum_eff_knocks(&metab_network);



        double start_enum, end_enum;
        
        //is direct enumeration requested
        if (options.get_algorithm().compare("direct")==0) {

                cout << endl << "\t"<<util::get_time_str()<<": direct enumeration..." <<endl;
                util::current_time(&start_enum);
                enum_eff_knocks.enum_erk_direct();              
                cout << endl << "\t"<<util::get_time_str()  << ": (pid="<<proc_id<<") # accepted ERK: "<<enum_eff_knocks.get_erk_map().size();
                util::current_time(&end_enum);
                enum_eff_knocks.set_erk_enum_time(end_enum-start_enum);
                enum_eff_knocks.print_erk(ko_fname);

                
                cout << endl << "\t"<<util::get_time_str()  << ": ERKs enumerated in "<< (end_enum-start_enum)<<" seconds";

        
        } else {
        //is indirect enumeration requested

                cout << endl << "\t"<<util::get_time_str()<<": indirect enumeration..." <<endl;
                
                util::current_time(&start_enum);
                
                //enumerated UFES
                enum_eff_knocks.enum_ufes();
                //exchange UFES subsets between compute nodes
                enum_eff_knocks.communicate_ufes_map();
                cout << endl << "\t"<<util::get_time_str()  << ": (pid="<<proc_id<<") # accepted UFES: "<<enum_eff_knocks.get_ufes_map().size();
                //cout << endl << "\t"<<util::get_time_str()  << ": (pid="<<proc_id<<") # accepted UFES: "<<enum_eff_knocks.get_ufes_hash().size();

                #ifdef PARALLEL         
                        MPI_Barrier(MPI_COMM_WORLD);
                #endif
                util::current_time(&end_enum);
                enum_eff_knocks.set_ufes_enum_time(end_enum-start_enum);
                cout << endl << "\t"<<util::get_time_str()  << ": UFES enumerated in "<< (end_enum-start_enum)<<" seconds";
                //enum_eff_knocks.print_ufes("ufes.txt");
                util::current_time(&start_enum);
                enum_eff_knocks.enum_erk();
                enum_eff_knocks.communicate_erk_map();

                cout << endl << "\t"<<util::get_time_str()  << ": (pid="<<proc_id<<") # accepted ERK: "<<enum_eff_knocks.get_erk_map().size();
                util::current_time(&end_enum);
                cout << endl << "\t"<<util::get_time_str()  << ": ERKs enumerated in "<< (end_enum-start_enum)<<" seconds";

                enum_eff_knocks.set_erk_enum_time(end_enum-start_enum);
                enum_eff_knocks.print_erk(ko_fname);
                //if (proc_id==0)
                //      cout << endl << "\t"<<util::get_time_str()<<": done"<<endl;
        }

        #ifdef PARALLEL         
                MPI_Barrier(MPI_COMM_WORLD);
                MPI_Finalize(); 
        #endif
        return 0;

}