// -----------------------------------------------------------------------------------------------------
// Copyright (c) 2006-2020, Knut Reinert & Freie Universität Berlin
// Copyright (c) 2016-2020, Knut Reinert & MPI für molekulare Genetik
// This file may be used, modified and/or redistributed under the terms of the 3-clause BSD-License
// shipped with this file and also available at: https://github.com/seqan/seqan3/blob/master/LICENSE.md
// -----------------------------------------------------------------------------------------------------

#include <sstream>
#include <string>

#include <gtest/gtest.h>

#include <seqan3/alphabet/nucleotide/dna15.hpp>
#include <seqan3/io/sequence_file/all.hpp>
#include <seqan3/std/algorithm>
#include <seqan3/std/ranges>

#include "sequence_file_format_test_template.hpp"

template <>
struct sequence_file_read<seqan3::format_fasta> : public sequence_file_data
{
    std::string standard_input
    {
        "> ID1\n"
        "ACGTTTTTTTTTTTTTTT\n"
        "> ID2\n"
        "ACGTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT\n"
        "> ID3 lala\n"
        "ACGTTTA\n"
    };

    std::string illegal_alphabet_character_input
    {
        "> ID1\n"
        "ACGPTTTTTTTTTTTTTT\n"
        "> ID2\n"
        "ACGTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT\n"
        "> ID3 lala\n"
        "ACGTTTA\n"
    };

    std::string standard_output
    {
        "> ID1\n"
        "ACGTTTTTTTTTTTTTTT\n"
        "> ID2\n"
        "ACGTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT\nTT\n"
        //                                             linebreak inserted after 80 char  ^
        "> ID3 lala\n"
        "ACGTTTA\n"
    };

    std::string no_or_ill_formatted_id_input
    {
        "! ID1\n"
        "ACGTTTTTTTTTTTTTTT\n"
    };
};

// ---------------------------------------------------------------------------------------------------------------------
// parametrized tests
// ---------------------------------------------------------------------------------------------------------------------

INSTANTIATE_TYPED_TEST_SUITE_P(fasta, sequence_file_read, seqan3::format_fasta, );
INSTANTIATE_TYPED_TEST_SUITE_P(fasta, sequence_file_write, seqan3::format_fasta, );

// ----------------------------------------------------------------------------
// reading
// ----------------------------------------------------------------------------

struct read : public sequence_file_data
{
    seqan3::sequence_file_input_options<seqan3::dna15, false> options{};

    std::string id;
    seqan3::dna5_vector seq;

    void do_read_test(std::string const & input)
    {
        std::stringstream istream{input};

        seqan3::sequence_file_input fin{istream, seqan3::format_fasta{}, seqan3::fields<seqan3::field::id,
                                                                                        seqan3::field::seq>{}};
        fin.options = options;

        auto it = fin.begin();
        for (unsigned i = 0; i < 3; ++i, ++it)
        {
            EXPECT_RANGE_EQ(seqan3::get<seqan3::field::seq>(*it), seqs[i]);
            EXPECT_EQ(seqan3::get<seqan3::field::id>(*it), ids[i]);
        }
    }
};

TEST_F(read, newline_before_eof)
{
    std::string input
    {
        "> ID1\n"
        "ACGTTTTTTTTTTTTTTT\n"
        "> ID2\n"
        "ACGTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT\n"
        "> ID3 lala\n"
        "ACGTTTA"
    };
    do_read_test(input);
}

TEST_F(read, noblank_before_id)
{
    std::string input
    {
        ">ID1\n"
        "ACGTTTTTTTTTTTTTTT\n"
        ">ID2\n"
        "ACGTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT\n"
        ">ID3 lala\n"
        "ACGTTTA\n"
    };
    do_read_test(input);
}

TEST_F(read, whitespace_in_seq)
{
    std::string input
    {
        "> ID1\n"
        "ACGTTTT\n\nTTTTTTTTTTT\n"
        "\n"
        "> ID2\n"
        "ACGTTTT\t\tTTTTTTTTTTT\t\nTTTTTTTTTTT\vTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT\rTTTTTTTTTTTTTTTTT\n"
        "> ID3 lala\n"
        "ACGT\fTTA\n"
    };
    do_read_test(input);
}

TEST_F(read, digits_in_seq)
{
    std::string input
    {
        "> ID1\n"
        "10  ACGTTTTTTTTTTTTTTT\n"
        "> ID2\n"
        "  80 ACGTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT  900"
        "1000 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT\n"
        "> ID3 lala\n"
        "ACGT9T5T2A\n"
    };
    do_read_test(input);
}

TEST_F(read, old_id_style)
{
    std::string input
    {
        "; ID1\n"
        "ACGTTTTTTTTTTTTTTT\n"
        "; ID2\n"
        "ACGTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT\n"
        "; ID3 lala\n"
        "ACGTTTA\n"
    };

    do_read_test(input);
}

TEST_F(read, mixed_issues)
{
    std::string input
    {
        "> ID1\n"
        "ACGTTTT\n\nTTTTTTTTTTT\n"
        "\n"
        ";ID2\n"
        "ACGTTTT\t75\tTTTTTTTTTTT\t\nTTTTTTTTTTT9\vTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT\rTTTTTTTTTTTTTTTTT\n"
        "> ID3 lala\n"
        "ACGT\fTTA"
    };
    do_read_test(input);
}

// ----------------------------------------------------------------------------
// writing
// ----------------------------------------------------------------------------

struct write : public ::testing::Test
{
    std::vector<seqan3::dna5_vector> seqs
    {
        "ACGT"_dna5,
        "AGGCTGNAGGCTGNAGGCTGNAGGCTGNAGGCTGNAGGCTGNAGGCTGNAGGCTGNAGGCTGNAGGCTGNAGGCTGNAGGCTGNAGGCTGN"_dna5,
        "GGAGTATAATATATATATATATAT"_dna5
    };

    std::vector<std::string> ids
    {
        "TEST 1",
        "Test2",
        "Test3"
    };

    seqan3::sequence_file_output_options options{};

    std::ostringstream ostream;

    void do_write_test()
    {
        seqan3::sequence_file_output fout{ostream, seqan3::format_fasta{}, seqan3::fields<seqan3::field::seq,
                                                                                          seqan3::field::id>{}};
        fout.options = options;

        for (unsigned i = 0; i < 3; ++i)
            EXPECT_NO_THROW(( fout.emplace_back(seqs[i], ids[i]) ));

        ostream.flush();
    }
};

TEST_F(write, options_letters_per_line)
{
    options.fasta_letters_per_line = 7;

    std::string comp
    {
        "> TEST 1\n"
        "ACGT\n"
        "> Test2\n"
        "AGGCTGN\nAGGCTGN\nAGGCTGN\nAGGCTGN\nAGGCTGN\nAGGCTGN\nAGGCTGN\nAGGCTGN\nAGGCTGN\nAGGCTGN\nAGGCTGN\nAGGCTGN\n"
        "AGGCTGN\n"
        "> Test3\n"
        "GGAGTAT\nAATATAT\nATATATA\nTAT\n"
    };

    do_write_test();

    EXPECT_EQ(ostream.str(), comp);
}

TEST_F(write, options_legacy_id_marker)
{
    options.fasta_legacy_id_marker = true;

    std::string comp
    {
        "; TEST 1\n"
        "ACGT\n"
        "; Test2\n"
        "AGGCTGNAGGCTGNAGGCTGNAGGCTGNAGGCTGNAGGCTGNAGGCTGNAGGCTGNAGGCTGNAGGCTGNAGGCTGNAGG\nCTGNAGGCTGN\n"
        //                                             linebreak inserted after 80 char  ^
        "; Test3\n"
        "GGAGTATAATATATATATATATAT\n"
    };

    do_write_test();

    EXPECT_EQ(ostream.str(), comp);
}

TEST_F(write, options_blank_before_id)
{
    options.fasta_blank_before_id = false;

    std::string comp
    {
        ">TEST 1\n"
        "ACGT\n"
        ">Test2\n"
        "AGGCTGNAGGCTGNAGGCTGNAGGCTGNAGGCTGNAGGCTGNAGGCTGNAGGCTGNAGGCTGNAGGCTGNAGGCTGNAGG\nCTGNAGGCTGN\n"
        //                                             linebreak inserted after 80 char  ^
        ">Test3\n"
        "GGAGTATAATATATATATATATAT\n"
    };

    do_write_test();

    EXPECT_EQ(ostream.str(), comp);
}

TEST_F(write, options_add_carriage_return)
{
    options.add_carriage_return = true;

    std::string comp
    {
        "> TEST 1\r\n"
        "ACGT\r\n"
        "> Test2\r\n"
        "AGGCTGNAGGCTGNAGGCTGNAGGCTGNAGGCTGNAGGCTGNAGGCTGNAGGCTGNAGGCTGNAGGCTGNAGGCTGNAGG\r\nCTGNAGGCTGN\r\n"
        //                                             linebreak inserted after 80 char  ^
        "> Test3\r\n"
        "GGAGTATAATATATATATATATAT\r\n"
    };

    do_write_test();

    EXPECT_EQ(ostream.str(), comp);
}

TEST_F(write, options_all)
{
    options.add_carriage_return = true;
    options.fasta_blank_before_id = false;
    options.fasta_legacy_id_marker = true;
    options.fasta_letters_per_line = 21;

    std::string comp
    {
        ";TEST 1\r\n"
        "ACGT\r\n"
        ";Test2\r\n"
        "AGGCTGNAGGCTGNAGGCTGN\r\nAGGCTGNAGGCTGNAGGCTGN\r\nAGGCTGNAGGCTGNAGGCTGN\r\nAGGCTGNAGGCTGNAGGCTGN\r\n"
        "AGGCTGN\r\n"
        ";Test3\r\n"
        "GGAGTATAATATATATATATA\r\nTAT\r\n"
    };
    do_write_test();

    EXPECT_EQ(ostream.str(), comp);
}