#include <iostream>
#include <fstream>
#include <sstream>
#include <string>
#include <vector>

using namespace std;

// Class to store fasta objects
class Fasta
{
    private:
        string name;
        string sequence;
    public:
        Fasta(string n, string s)
        {
            name = n;
            sequence = s;
        }
        void set_name(string n) { name = n; }
        void set_sequence(string s) { sequence = s; }
        void print_sequence() { cout << ">" << name << "\n" << sequence << "\n"; }
};

// Parse fasta file and return Fasta objects to a vector<Fasta> pointer
void fasta_parser(vector<Fasta> * sequences, string filename)
{
    std::ifstream infile(filename);
    if ( !infile.is_open() )
         cout<<"Could not open file\n";
    else {
        string line;
        string name;
        string sequence;

        while (std::getline(infile, line))
        {
            if (line[0] == '>')
            {
                name = line.erase(0, 1);
            }
            else
            {
                sequence = line;
                Fasta seq = Fasta(name, sequence);
                sequences -> push_back(seq);
            }
        }
    }
}

int main(int argc, char *argv[])
{
    string filename;

    // Parse user input
    if (argc != 2)
    {
        cout << "Usage: ./oop input_fasta_file\n";
        return 1;
    }
    else
    {
        filename = argv[1];
    }

    // Parse fasta file
    vector<Fasta> sequences;
    fasta_parser(&sequences, filename);

    for (Fasta s : sequences)
    {
        s.print_sequence();
    }

    return 0;
}