#include <iostream>
#include <vector>
#include <getopt.h>
#include <cstring>

#include "dnacol.h"
#include "dna_scanning.h"
#include "dnastats.h"
#include "dna.h"
#include "string_tools.h"

#include <unistd.h>

std::string OutfilePrefix;
std::string DataDirectory;
std::vector<std::string> Species;
std::vector<std::string> DNA;

static struct option long_options[] = {
    {"species-names", required_argument, 0, 'n'},
    {"sequence-files", required_argument, 0, 's'},
    {"data-directory", required_argument, 0, 't'},
    {"outfile-prefix", required_argument, 0, 'o'},
    {0,0,0,0}
};

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

    int c;
    while(1)
    {
        int option_index = 0;
        c = getopt_long(argc, argv, "n:s:t:o:", long_options, &option_index);

        if (c == -1) break;

        switch(c)
        {
        case 'n': 
            Species = split_token(optarg, strlen(optarg), ","); 
            break;
        case 's': 
            DNA = split_token(optarg, strlen(optarg), ","); 
            break;
        case 't': 
            DataDirectory = std::string(optarg); 
            break;
        case 'o': 
            OutfilePrefix = std::string(optarg); 
            break;
        default:
            printf("Usage: make_dnas_file -n <species_names> -s <sequence_files> -t <data_directory>"
                   "-o <outfile_prefix>\n"
                   "<species_names>: comma separated list of species names (no spaces)\n"
                   "<sequence_files>: comma separated list of sequence files (no spaces)\n"
                   "<data_directory>: directory containing all sequence files\n"
                   "<outfile_prefix>: prefix on output files\n");
            exit(1); break;
      
        }
    }

    if (OutfilePrefix.empty())
    {
        fprintf(stderr, "Please provide an output file prefix (option -o)\n");
        exit(53);
    }

	
    //parse dna from SequenceFile, build a dna_collection from it
    if (Species.size() != DNA.size()) 
    {
        fprintf(stderr, "You must have the same number of species names as ");
        fprintf(stderr, "genomic sequence files.\n");
        exit(53);
    }

    cis::dna_collection dnac;
    for (size_t g=0; g < DNA.size(); g++)
    {
        try 
        {
            printf("Parsing %s genomic sequence file...\n", DNA[g].c_str());
            dnac.add(Species[g], DataDirectory, DNA[g]);
        }
        catch (string &msg)
        { 
            fprintf(stderr, "%s", msg.c_str()); return 2; 
        }
    }

    dnac.calc_offsets();
    dnac.open_dnas();

    string dnasrc(OutfilePrefix); 
    std::ofstream dnafile;
    dnafile.open(dnasrc.c_str());

    for (cis::DNAS::iterator dnac_it = dnac.begin(); dnac_it != dnac.end(); ++dnac_it) 
    dnafile<<*(*dnac_it)<<endl;
    dnafile.close();

    return 0;
}