#pragma once

#include <vector>
#include <fstream>
#include <sstream>
#include <stdexcept>
#include <string>
#include <unordered_map>

#include "GeneticCode.hpp"
#include "strutils.hpp"


class Sequence{

public:
    Sequence(std::string sequence) {
        this->sequence = sequence;
    }

    unsigned int get_length() {
        return this->sequence.length();
    }

    std::string get_sequence() {
        return this->sequence;
    }

protected:
    std::string sequence;
};


class ProteinSequence: public Sequence {

    using Sequence::Sequence;
};

class RNASequence: public Sequence {

    using Sequence::Sequence;

public:

    ProteinSequence translate_to_protein() {
        GeneticCode *code = GeneticCode::GetInstance();
        std::string protein_sequence = "";
        for (unsigned int i=0; i < this->sequence.length()-2; i+=3) {
            std::string codon = this->sequence.substr(i, 3);
            char amino_acid = code->get_amino_acid(codon);
            protein_sequence += amino_acid;
        }
        return ProteinSequence(protein_sequence);
    }
};

class DNASequence: public Sequence {

    using Sequence::Sequence;
public:
    DNASequence get_complement() {
        std::string complement = "";
        for (char &c: this->sequence) {
            complement += DNASequence::complement(c);
        }
        return DNASequence(complement);
    }

    static char complement(char c) {
        if (c == 'A') {
            return 'T';
        } else if (c == 'T') {
            return 'A';
        } else if (c == 'G') {
            return 'C';
        } else if (c == 'C') {
            return 'G';
        } else {
            throw std::invalid_argument("Error: nucleotide " + std::to_string(c) + " has no complement");
        }
    }

    RNASequence transcribe_to_rna() {
        std::string rna_sequence = this->sequence.substr(0);
        replace_all(rna_sequence, 'T', 'U');
        return RNASequence(rna_sequence);
    }


    
};