#include "math.h"

#include <map>
#include <sys/types.h>
#include <cstdlib>
#include <stdio.h>
#include <errno.h>
#include <string>
#include <iostream>
#include <fstream>
#include <vector>
#include <sstream>
#include <algorithm>

using namespace std;

struct SeedStruct {
    string id;
};

typedef vector<SeedStruct> seed_array;

// g++ complete_linkage

int main(int argc, char *argv[]) {
    seed_array seedstructarray;
    vector<seed_array> doublestructarray;
    vector<seed_array> tmp_doublestructarray;

    map<string, float> idmap;
    map<string, float>::iterator itid;

    map<string, float> idpairmap;
    map<string, float>::iterator itidpair;

    // add infile
    string infile = argv[1];
    char* infname = const_cast<char*>(infile.c_str());

    ifstream in(infname);
    string tmp_str;

    for (; getline(in, tmp_str, '\n');) {
        istringstream intmpstr(tmp_str);
        string tmp_id1, tmp_id2, tmp_dist;
        float dist;

        getline(intmpstr, tmp_id1, ' ');
        idmap[tmp_id1] = 1.0;
        getline(intmpstr, tmp_id2, ' ');
        idmap[tmp_id2] = 1.0;

        string tmp_idpair = tmp_id1 + "\t" + tmp_id2;
        getline(intmpstr, tmp_dist, ' ');
        dist = float(atof(tmp_dist.c_str()));
        idpairmap[tmp_idpair] = dist;
    }

    for (itid = idmap.begin(); itid != idmap.end(); ++itid) {
        SeedStruct tmp_seedstruct;
        tmp_seedstruct.id = itid->first;
        seedstructarray.push_back(tmp_seedstruct);
    }

    for (unsigned long int i = 0; i < seedstructarray.size(); ++i) {
        vector<SeedStruct> tmp;
        tmp.push_back(seedstructarray[i]);
        doublestructarray.push_back(tmp);
    }

    string str_cutoff_str = argv[2];
    float cutoff = float(atof(str_cutoff_str.c_str()));
    int loop = 0;

    for (; loop == 0;) {
        float mindist = 999999;
        unsigned long int currenti = 0, currentj = 0;

        for (unsigned long int i = 0; i < doublestructarray.size() - 1; ++i) {
            vector<SeedStruct> tmpvector1 = doublestructarray[i];
            for (unsigned long int j = i + 1; j < doublestructarray.size() - 1; ++j) {
                vector<SeedStruct> tmpvector2 = doublestructarray[j];

                float maxdist = 0;
                for (unsigned long int k = 0; k < tmpvector1.size(); ++k) {
                    string id1 = tmpvector1[k].id;
                    for (unsigned long int l = 0; l < tmpvector2.size(); ++l) {
                        string id2 = tmpvector2[l].id;
                        string idpair = id1 + "\t" + id2;
                        float dist = 0;

                        if (idpairmap.find(idpair) != idpairmap.end()) {
                            itidpair = idpairmap.find(idpair);
                            dist = itidpair->second;
                        }

                        if (maxdist < dist) {
                            maxdist = dist;
                        }
                    }
                }
                // End of inner for.

                if (maxdist < mindist) {
                    mindist = maxdist;
                    currenti = i;
                    currentj = j;
                }
            }
        }
        // End of outer for.

        if (mindist <= cutoff) {
            vector<SeedStruct> tmpvector = doublestructarray[currentj];
            for (unsigned long int i = 0; i < tmpvector.size(); ++i) {
                doublestructarray[currenti].push_back(tmpvector[i]);
            }

            for (unsigned long int i = 0; i < doublestructarray.size(); ++i) {
                if (i != currentj) {
                    tmp_doublestructarray.push_back(doublestructarray[i]);
                }
            }

            doublestructarray.clear();
            for (unsigned long int i = 0; i < tmp_doublestructarray.size(); ++i) {
                doublestructarray.push_back(tmp_doublestructarray[i]);
            }

            tmp_doublestructarray.clear();
        }
        else {
            loop = 1;
        }
    }
    // Main while cycle is over.

    std::cout << "First part time is: " << mid_time - start_time << "\n";
    std::cout << "Second part time is: " << end_time - mid_time << "\n";

    ofstream outfile;
    outfile.open(argv[3]);

    for (unsigned long int i = 0; i < doublestructarray.size(); ++i) {
        vector<SeedStruct> tmpvector = doublestructarray[i];
        string* id_array = new string[tmpvector.size()];
        for (unsigned long int j = 0; j < tmpvector.size(); ++j) {
        id_array[j] = tmpvector[j].id;
    }

    for (unsigned long int j = 0; j < tmpvector.size(); ++j) {
        outfile << id_array[j] << "\t";
    }

    outfile << endl;
    delete id_array;
    }

    outfile.close();
}