// SPDX-FileCopyrightText: 2006-2024 Knut Reinert & Freie Universität Berlin
// SPDX-FileCopyrightText: 2016-2024 Knut Reinert & MPI für molekulare Genetik
// SPDX-License-Identifier: CC0-1.0

#include <filesystem> // to create tmp directory

#include <seqan3/alphabet/nucleotide/dna4.hpp> // to create right datastructure in tmp file
#include <seqan3/core/debug_stream.hpp>        // for debug_stream
#include <seqan3/io/sequence_file/output.hpp>  // to create tmp file

// This creates a temporary file to ensure that the snippet works correctly without any dependency on external files.

struct write_file_dummy_struct
{
    std::filesystem::path const file_path = std::filesystem::temp_directory_path() / "seq.fasta";

    write_file_dummy_struct()
    {

        auto file_raw = R"//![fasta_file](
>seq1
ACGTGATG
>seq2
AGTGATACT
)//![fasta_file]";

        std::ofstream file{file_path};
        std::string str{file_raw};
        file << str.substr(1); // skip first newline
    }

    ~write_file_dummy_struct()
    {
        std::error_code ec{};
        std::filesystem::remove(file_path, ec);

        if (ec)
            seqan3::debug_stream << "[WARNING] Could not delete " << file_path << ". " << ec.message() << '\n';
    }
};

write_file_dummy_struct go{};

//! [fileinput]
#include <string>

#include <seqan3/core/debug_stream.hpp>      // for debug_stream
#include <seqan3/io/sequence_file/input.hpp> // for sequence_file_input

int main()
{
    std::filesystem::path tmp_dir = std::filesystem::temp_directory_path(); // get the tmp directory

    // Initialise a file input object with a FASTA file.
    seqan3::sequence_file_input file_in{tmp_dir / "seq.fasta"};

    // Retrieve the sequences and ids.
    for (auto & [seq, id, qual] : file_in)
    {
        seqan3::debug_stream << "ID:     " << id << '\n';
        seqan3::debug_stream << "SEQ:    " << seq << '\n';
        seqan3::debug_stream << "Empty Qual." << qual << '\n'; // qual is empty for FASTA files
    }

    return 0;
}
//! [fileinput]
