/***
        Biorseo, Louis Becquey, nov 2018-nov 2021
        Special thanks to Lénaic Durand and Nathalie Bertrand for working a lot on version 2.0
        louis.becquey@univ-evry.fr (likely expired email account, find me on the internet)
***/
#include <cmath> 

#include <algorithm>
#include <boost/program_options.hpp>
#include <cstdlib>
#include <iostream>
#include <iterator>
#include <string>
#include <vector>

#include "MOIP.h"
#include "Motif.h"
#include "fa.h"

using namespace std;
namespace po = boost::program_options;

string remove_ext(const char* mystr, char dot, char sep)
{
    // COPYPASTA from stackoverflow

    char *retstr, *lastdot, *lastsep;

    // Error checks and allocate string.
    if (mystr == nullptr) return nullptr;
    if ((retstr = static_cast<char*>(malloc(strlen(mystr) + 1))) == nullptr) return nullptr;

    // Make a copy and find the relevant characters.
    strcpy(retstr, mystr);
    lastdot = strrchr(retstr, dot);
    lastsep = (sep == 0) ? nullptr : strrchr(retstr, sep);

    // If it has an extension separator.
    if (lastdot != nullptr) {
        // and it's before the extenstion separator.
        if (lastsep != nullptr) {
            if (lastsep < lastdot) {
                // then remove it.
                *lastdot = '\0';
            }
        } else {
            // Has extension separator with no path separator.
            *lastdot = '\0';
        }
    }

    // Return the modified string.
    return string(retstr);
}

int main(int argc, char* argv[])
{
    /*  VARIABLE DECLARATIONS  */

    string             inputName, outputName, motifs_path_name, basename;
    bool               verbose = false;
    float              theta_p_threshold;
    char               obj_function_nbr;
    char               mea_or_mfe = 'b'; // a for MFE, b for MEA
    list<Fasta>        f;
    ofstream           outfile;
    SecondaryStructure bestSSO1, bestSSO2;
    RNA                myRNA;

    /*  ARGUMENT CHECKING  */
    
    po::options_description desc("Options");
    desc.add_options()
    ("help,h", "Print the help message")
    ("version", "Print the program version")
    ("seq,s", po::value<string>(&inputName)->required(), "Fasta file containing the RNA sequence")
    ("descfolder,d", po::value<string>(&motifs_path_name), "A folder containing modules in .desc format, as produced by Djelloul & Denise's catalog program")
    ("rinfolder,x", po::value<string>(&motifs_path_name), "A folder containing CaRNAval's RINs in .txt format, as produced by script transform_caRNAval_pickle.py")
    ("jsonfolder,a", po::value<string>(&motifs_path_name), "A folder containing a custom motif library in .json format")
    
    ("jar3dcsv,j",          po::value<string>(&motifs_path_name), "A file containing the output of JAR3D's search for motifs in the sequence, as produced by biorseo.py")
    ("bayespaircsv,b",      po::value<string>(&motifs_path_name), "A file containing the output of BayesPairing's search for motifs in the sequence, as produced by biorseo.py")
    ("first-objective,c",   po::value<unsigned int>(&MOIP::obj_to_solve_)->default_value(2), "Objective to solve in the mono-objective portions of the algorithm")
    ("output,o",            po::value<string>(&outputName), "A file to summarize the computation results")
    ("theta,t",             po::value<float>(&theta_p_threshold)->default_value(1e-3, "0.001"), "Pairing probability threshold to consider or not the possibility of pairing")
    ("function,f",          po::value<char>(&obj_function_nbr)->default_value('B'), "What objective function to use to include motifs: square of motif size in nucleotides like "
    "RNA-MoIP (A), light motif size + high number of components (B), site score (C), light motif size + site score + high number of components (D)")
    
    ("mfe,E", "Minimize stacking energies as second criteria (should lead to MFE structure)")
    ("mea,A", "(default) Maximize expected accuracy as second criteria (should lead to MEA structure)")

    ("disable-pseudoknots,n", "Add constraints forbidding the formation of pseudoknots")
    ("limit,l", po::value<unsigned int>(&MOIP::max_sol_nbr_)->default_value(500), "Intermediate number of solutions in the Pareto set above which we give up the calculation.")
    ("verbose,v", "Print what is happening to stdout");
    po::variables_map vm;
    po::store(po::parse_command_line(argc, argv, desc), vm);
    basename = remove_ext(inputName.c_str(), '.', '/');

    try {
        po::store(po::parse_command_line(argc, argv, desc), vm);    // can throw
        po::notify(vm);

        if (vm.count("help") or vm.count("-h")) {
            cout << "Biorseo, bio-objective integer linear programming framework to predict RNA secondary "
                    "structures by including known RNA modules."
                 << endl
                 << "developped by Louis Becquey, 2018-2021" << endl
                 << "Lénaïc Durand, 2019" << endl
                 << "Nathalie Bernard, 2021" << endl
                 << endl
                 << desc << endl;
            return EXIT_SUCCESS;
        }
        if (vm.count("version")) {
            cout << "Biorseo v2.1, dockerized, November 2021" << endl;
            return EXIT_SUCCESS;
        }
        if (vm.count("mfe")) mea_or_mfe = 'a';
        if (vm.count("mea")) mea_or_mfe = 'b';
        if (vm.count("verbose")) verbose = true;
        if (vm.count("disable-pseudoknots")) MOIP::allow_pk_ = false;

        if (!vm.count("jar3dcsv") and !vm.count("bayespaircsv") and !vm.count("descfolder") and !vm.count("rinfolder") and !vm.count("jsonfolder")) {
            cerr << "\033[31mYou must provide at least one of --descfolder, --rinfolder, --jsonfolder, --jar3dcsv or --bayespaircsv.\033[0m See --help "
                    "for more information."
                 << endl;
            return EXIT_FAILURE;
        }

        if ((vm.count("descfolder") or vm.count("jsonfolder") or vm.count("rinfolder")) and (obj_function_nbr == 'C' or obj_function_nbr == 'D')) {
            cerr << "\033[31mYou must provide --jar3dcsv or --bayespaircsv to use --function C or --function D.\033[0m See "
                    "--help for more information."
                 << endl;
            return EXIT_FAILURE;
        }

        po::notify(vm);    // throws on error, so do after help in case there are any problems
    } catch (po::error& e) {
        cerr << "ERROR: \033[31m" << e.what() << "\033[0m" << endl;
        cerr << desc << endl;
        return EXIT_FAILURE;
    }

    MOIP::obj_function_nbr_ = obj_function_nbr;
    MOIP::obj_function2_nbr_ = mea_or_mfe;

    /*  FILE PARSING  */

    // load fasta file
    if (verbose) cout << "Reading input files..." << endl;
    if (access(inputName.c_str(), F_OK) == -1) {
        cerr << "\033[31m" << inputName << " not found\033[0m" << endl;
        return EXIT_FAILURE;
    }
    Fasta::load(f, inputName.c_str());
    list<Fasta>::iterator fa = f.begin();
    if (verbose) cout << "loading " << fa->name() << "..." << endl;
    myRNA = RNA(fa->name(), fa->seq(), verbose);
    if (verbose) cout << "\t> " << inputName << " successfuly loaded (" << myRNA.get_RNA_length() << " nt)" << endl;

    // load CSV file
    if (access(motifs_path_name.c_str(), F_OK) == -1) {
        cerr << "\033[31m" << motifs_path_name << " not found\033[0m" << endl;
        return EXIT_FAILURE;
    }


    /*  FIND PARETO SET  */
    string source;
    if (vm.count("jar3dcsv"))
        source = "jar3dcsv";
    else if (vm.count("bayespaircsv"))
        source = "bayespaircsv";
    else if (vm.count("rinfolder"))
        source = "rinfolder";
    else if (vm.count("descfolder"))
        source = "descfolder";
    else if (vm.count("jsonfolder"))
        source = "jsonfolder";
    else
        cerr << "ERR: no source of modules provided !" << endl;
    
    MOIP               myMOIP = MOIP(myRNA, source, motifs_path_name.c_str(), theta_p_threshold, verbose);
    double             min, max;
    IloConstraintArray F(myMOIP.get_env());

    if (verbose)
        cout << "Solving..." << endl;
    try {
        bestSSO1 = myMOIP.solve_objective(1, -__DBL_MAX__, __DBL_MAX__);
        if (verbose) cout << endl;
        bestSSO2 = myMOIP.solve_objective(2, -__DBL_MAX__, __DBL_MAX__);
        if (verbose) {
            cout << endl << "Best solution according to objective 1 :" << bestSSO1.to_string() << endl;
            cout << "Best solution according to objective 2 :" << bestSSO2.to_string() << endl;
        }

        // extend the Pareto set on top
        if (MOIP::obj_to_solve_ == 1) {
            myMOIP.add_solution(bestSSO1);
            min = bestSSO1.get_objective_score(2) + MOIP::precision_;
            max = bestSSO2.get_objective_score(2) + MOIP::precision_;
            if (verbose) cout << endl << "Solving obj1 on top of best solution 1." << endl;
        } else {
            myMOIP.add_solution(bestSSO2);
            min = bestSSO2.get_objective_score(1) + MOIP::precision_;
            max = bestSSO1.get_objective_score(1) + MOIP::precision_;
            if (verbose) cout << endl << "Solving obj2 on top of best solution 2." << endl;
        }

        if (verbose)
            cout << setprecision(-log10(MOIP::precision_) + 4) << "\nSolving objective function " << MOIP::obj_to_solve_ << ", on top of "
                 << min << ": Obj" << 3 - MOIP::obj_to_solve_ << "  being in [" << min << ", " << max << "]..." << endl;
        myMOIP.search_between(min, max);

        // extend the Pareto set below
        if (MOIP::obj_to_solve_ == 1) {
            if (verbose) cout << endl << "Solving obj1 below best solution 1." << endl;
            min = -__DBL_MAX__;
            max = bestSSO1.get_objective_score(2);
        } else {
            if (verbose) cout << endl << "Solving obj2 below best solution 2." << endl;
            min = -__DBL_MAX__;
            max = bestSSO2.get_objective_score(1);
        }
        if (verbose)
            cout << setprecision(-log10(MOIP::precision_) + 4) << "\nSolving objective function " << MOIP::obj_to_solve_
                 << ", below (or eq. to) " << max << ": Obj" << 3 - MOIP::obj_to_solve_ << "  being in [" << min << ", "
                 << max << "]..." << endl
                 << "\t> Forbidding " << F.getSize() << " solutions found in [" << setprecision(10)
                 << min - MOIP::precision_ << ", " << max + MOIP::precision_ << ']' << endl;
        myMOIP.search_between(min, max);

    } catch (IloCplex::Exception& e) {
        cerr << "\033[31mCplex Exception: " << e.getMessage() << "\033[0m" << endl;
        exit(EXIT_FAILURE);
    }

    /*  DISPLAY RESULTS  */

    // print the pareto set
    if (verbose) {
        cout << endl << endl << "---------------------------------------------------------------" << endl;
        cout  << "Whole Pareto Set:" << endl;
        for (uint i = 0; i < myMOIP.get_n_solutions(); i++) myMOIP.solution(i).print();
        cout << endl;
        cout << myMOIP.get_n_candidates() << " candidate insertion sites, " << myMOIP.get_n_solutions() << " solutions kept." << endl;
        cout << "Best value for Motif insertion objective: " << bestSSO1.get_objective_score(1) << endl;
        cout << "Best value for structure expected accuracy: " << bestSSO2.get_objective_score(2) << endl;
    }

    // Save it to file
    if (vm.count("output")) {
        if (verbose) cout << "Saving structures to " << outputName << "..." << endl;
        outfile.open(outputName);
        outfile << fa->name() << endl << fa->seq() << endl;
        for (uint i = 0; i < myMOIP.get_n_solutions(); i++) {
            outfile << myMOIP.solution(i).to_string() << endl << structure_with_contacts(myMOIP.solution(i)) << endl;
            string str1 = myMOIP.solution(i).to_string();

            // Check if the best score for obj2 is actually included in the results
            // string delimiter = "\t";
            // string obj2 = str1.substr(str1.find(delimiter) + delimiter.size());
            // obj2 = obj2.substr(0, obj2.find(delimiter));
            // if (obj2.compare(best_score) == 0)
            //    flag = true;*/
        }
        // if (!flag)
        //     cout << "\033[1m\033[31mBest score not found for " << outputName << " !\033[0m" << endl;
        // else
        //     cout << "OK for "<< outputName << "!" << endl;

        outfile.close();
    }

    /*  QUIT  */

    return EXIT_SUCCESS;
}