// SPDX-FileCopyrightText: 2006-2024 Knut Reinert & Freie Universität Berlin
// SPDX-FileCopyrightText: 2016-2024 Knut Reinert & MPI für molekulare Genetik
// SPDX-License-Identifier: BSD-3-Clause

#include <gtest/gtest.h>

#include <iterator>
#include <sstream>

#include <seqan3/core/detail/all_view.hpp>
#include <seqan3/io/sequence_file/input.hpp>
#include <seqan3/io/sequence_file/output.hpp>

TEST(rows, assign_sequence_files)
{
    std::string const input{
        ">TEST 1\n"
        "ACGT\n"
        ">Test2\n"
        "AGGCTGN AGGCTGN AGGCTGN AGGCTGN AGGCTGN AGGCTGN AGGCTGN AGGCTGN AGGCTGN AGGCTGN AGGCTGN AGGCTGN AGGCTGN\n\n"
        ">Test3\n"
        "GGAGTATAATATATATATATATAT\n"};

    std::string const output_comp{
        ">TEST 1\n"
        "ACGT\n"
        ">Test2\n"
        "AGGCTGNAGGCTGNAGGCTGNAGGCTGNAGGCTGNAGGCTGNAGGCTGNAGGCTGNAGGCTGNAGGCTGNAGGCTGNAGGCTGNAGGCTGN\n"
        ">Test3\n"
        "GGAGTATAATATATATATATATAT\n"};

    seqan3::sequence_file_input fin{std::istringstream{input}, seqan3::format_fasta{}};
    seqan3::sequence_file_output fout{std::ostringstream{}, seqan3::format_fasta{}};
    fout.options.fasta_letters_per_line = 0;

    fout = fin;

    fout.get_stream().flush();
    EXPECT_EQ(reinterpret_cast<std::ostringstream &>(fout.get_stream()).str(), output_comp);
}

TEST(rows, assign_sequence_files_read_blanks)
{
    std::string const input{
        ">TEST 1\n"
        "ACGT\n"
        "> Test2\n"
        "AGGCTGNAGGCTGNAGGCTGNAGGCTGNAGGCTGNAGGCTGNAGGCTGNAGGCTGNAGGCTGNAGGCTGNAGGCTGNAGGCTGNAGGCTGN\n"
        ">  Test3\n"
        "GGAGTATAATATATATATATATAT\n"};

    std::string const expected_output = input;

    seqan3::sequence_file_input fin{std::istringstream{input}, seqan3::format_fasta{}};
    fin.options.fasta_ignore_blanks_before_id = false;

    seqan3::sequence_file_output fout{std::ostringstream{}, seqan3::format_fasta{}};
    fout.options.fasta_letters_per_line = 0;

    fout = fin;

    fout.get_stream().flush();
    std::string const output = reinterpret_cast<std::ostringstream &>(fout.get_stream()).str();
    EXPECT_EQ(output, expected_output);
}

TEST(integration, assign_sequence_file_pipes)
{
    std::string const input{">TEST1\n"
                            "ACGT\n"
                            ">Test2\n"
                            "AGGCTGNAGGCTGAGGCTGNAGGCTGNAGGCTGNAGGCTGNAGGCTGNAGGCTGNAGGCTGN\n"
                            ">Test3\n"
                            "GGAGTATAATATATATATATATAT\n"};

    // valid without assignment?
    seqan3::sequence_file_input{std::istringstream{input}, seqan3::format_fasta{}}
        | seqan3::sequence_file_output{std::ostringstream{}, seqan3::format_fasta{}};

    // valid with assignment and check contents
    auto fout = seqan3::sequence_file_input{std::istringstream{input}, seqan3::format_fasta{}}
              | seqan3::sequence_file_output{std::ostringstream{}, seqan3::format_fasta{}};

    fout.get_stream().flush();
    EXPECT_EQ(reinterpret_cast<std::ostringstream &>(fout.get_stream()).str(), input);
}

TEST(integration, view)
{
    std::string const input{">TEST1\n"
                            "ACGT\n"
                            ">Test2\n"
                            "AGGCTGNAGGCTGAGGCTGNAGGCTGNAGGCTGNAGGCTGNAGGCTGNAGGCTGNAGGCTGN\n"
                            ">Test3\n"
                            "GGAGTATAATATATATATATATAT\n"};

    std::string const output{">TEST1\n"
                             "ACGT\n"
                             ">Test2\n"
                             "AGGCTGNAGGCTGAGGCTGNAGGCTGNAGGCTGNAGGCTGNAGGCTGNAGGCTGNAGGCTGN\n"};

    // valid without assignment?
    seqan3::sequence_file_input{std::istringstream{input}, seqan3::format_fasta{}} | seqan3::detail::all
        | std::views::take(2) | seqan3::sequence_file_output{std::ostringstream{}, seqan3::format_fasta{}};

    // valid with assignment and check contents
    auto fout = seqan3::sequence_file_input{std::istringstream{input}, seqan3::format_fasta{}} | seqan3::detail::all
              | std::views::take(2) | seqan3::sequence_file_output{std::ostringstream{}, seqan3::format_fasta{}};

    fout.get_stream().flush();
    EXPECT_EQ(reinterpret_cast<std::ostringstream &>(fout.get_stream()).str(), output);
}

TEST(integration, convert_fastq_to_fasta)
{
    std::string const fastq_in{"@ID1\n"
                               "ACGTT\n"
                               "+\n"
                               "!##$%\n"
                               "@ID2\n"
                               "TATTA\n"
                               "+\n"
                               ",BDEB\n"};

    std::string const fasta_out{">ID1\n"
                                "ACGTT\n"
                                ">ID2\n"
                                "TATTA\n"};

    auto fout = seqan3::sequence_file_input{std::istringstream{fastq_in}, seqan3::format_fastq{}}
              | seqan3::sequence_file_output{std::ostringstream{}, seqan3::format_fasta{}};
    fout.get_stream().flush();
    EXPECT_EQ(reinterpret_cast<std::ostringstream &>(fout.get_stream()).str(), fasta_out);
}

TEST(integration, sequence_name_contains_id_tag)
{
    // The sequence id is '>TEST 1'.
    std::string const input{"> >TEST 1\n"
                            "ACGT\n"};

    std::string const expected_output{">>TEST 1\n"
                                      "ACGT\n"};

    seqan3::sequence_file_input fin{std::istringstream{input}, seqan3::format_fasta{}};
    seqan3::sequence_file_output fout{std::ostringstream{}, seqan3::format_fasta{}};
    fout = fin;

    fout.get_stream().flush();

    std::string const output = static_cast<std::ostringstream &>(fout.get_stream()).str();
    EXPECT_EQ(output, expected_output);
}
