// -----------------------------------------------------------------------------------------------------
// 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 <deque>
#include <tuple>
#include <vector>

#include <gtest/gtest.h>

#include <seqan3/alphabet/nucleotide/dna4.hpp>
#include <seqan3/core/bit_manipulation.hpp>
#include <seqan3/core/simd/simd_traits.hpp>
#include <seqan3/core/simd/simd.hpp>
#include <seqan3/core/simd/view_to_simd.hpp>
#include <seqan3/range/container/aligned_allocator.hpp>
#include <seqan3/range/views/type_reduce.hpp>
#include <seqan3/std/algorithm>
#include <seqan3/std/concepts>
#include <seqan3/std/iterator>
#include <seqan3/std/ranges>

#include <seqan3/test/performance/sequence_generator.hpp>
#include <seqan3/test/pretty_printing.hpp>
#include <seqan3/test/simd_utility.hpp>

template <typename t>
class view_to_simd_test : public ::testing::Test
{
public:
    using container_t = std::tuple_element_t<0, t>;
    using simd_t      = std::tuple_element_t<1, t>;
    using allocator_t = std::conditional_t<seqan3::simd::simd_traits<simd_t>::length == 1,
                                           std::allocator<simd_t>,
                                           seqan3::aligned_allocator<simd_t, sizeof(simd_t)>>;

    static constexpr size_t padding_value_dna4 = seqan3::alphabet_size<std::ranges::range_value_t<container_t>>;
    static constexpr size_t padding_value_custom = 8;
    static constexpr size_t max_sequence_length = seqan3::simd::simd_traits<simd_t>::length * 64;

    void SetUp()
    {
        sequences.resize(seqan3::simd::simd_traits<simd_t>::length);
        for (size_t i = 0; i < seqan3::simd::simd_traits<simd_t>::length; ++i)
        {
            // Generate sequences that end on different boundaries
            size_t l = max_sequence_length - (i * seqan3::simd::simd_traits<simd_t>::length) - i;
            std::ranges::copy(seqan3::test::generate_sequence<std::iter_value_t<container_t>>(l),
                              std::cpp20::back_inserter(sequences[i]));
        }

        transformed_simd_vec.resize(max_sequence_length, seqan3::simd::fill<simd_t>(padding_value_dna4));
        transformed_simd_vec_padded.resize(max_sequence_length, seqan3::simd::fill<simd_t>(padding_value_custom));

        for (size_t i = 0; i < seqan3::simd::simd_traits<simd_t>::length; ++i)
        {
            for (size_t j = 0; j < sequences[i].size(); ++j)
            {
                transformed_simd_vec[j][i] = seqan3::to_rank(sequences[i][j]);
                transformed_simd_vec_padded[j][i] = seqan3::to_rank(sequences[i][j]);
            }
        }
    }

    void compare(auto simd_view, auto cmp)
    {
        auto it_cmp = cmp.begin();
        size_t simd_view_size = 0;
        for (auto && chunk : simd_view)
        {
            simd_view_size += chunk.size();
            for (size_t i = 0; i < chunk.size(); ++i)
            {
                SIMD_EQ(chunk[i], *it_cmp);
                ++it_cmp;
            }
        }
        EXPECT_EQ(simd_view_size, cmp.size());
    }

    std::vector<container_t> sequences;
    std::vector<simd_t, allocator_t> transformed_simd_vec{};
    std::vector<simd_t, allocator_t> transformed_simd_vec_padded{};

    using view_to_simd_type = seqan3::detail::view_to_simd<seqan3::type_reduce_view<std::vector<container_t> &>,
                                                           simd_t>;
};

using test_types = ::testing::Types<std::tuple<std::vector<seqan3::dna4>, seqan3::simd::simd_type_t<int8_t>>,
                                    std::tuple<std::vector<seqan3::dna4>, seqan3::simd::simd_type_t<int16_t>>,
                                    std::tuple<std::vector<seqan3::dna4>, seqan3::simd::simd_type_t<int32_t>>,
                                    std::tuple<std::vector<seqan3::dna4>, seqan3::simd::simd_type_t<int64_t>>,
                                    std::tuple<std::vector<seqan3::dna4>, seqan3::simd::simd_type_t<uint8_t>>,
                                    std::tuple<std::vector<seqan3::dna4>, seqan3::simd::simd_type_t<uint16_t>>,
                                    std::tuple<std::vector<seqan3::dna4>, seqan3::simd::simd_type_t<uint32_t>>,
                                    std::tuple<std::vector<seqan3::dna4>, seqan3::simd::simd_type_t<uint64_t>>,
                                    std::tuple<std::deque<seqan3::dna4>, seqan3::simd::simd_type_t<int8_t>>,
                                    std::tuple<std::deque<seqan3::dna4>, seqan3::simd::simd_type_t<int16_t>>,
                                    std::tuple<std::deque<seqan3::dna4>, seqan3::simd::simd_type_t<int32_t>>,
                                    std::tuple<std::deque<seqan3::dna4>, seqan3::simd::simd_type_t<int64_t>>,
                                    std::tuple<std::deque<seqan3::dna4>, seqan3::simd::simd_type_t<uint8_t>>,
                                    std::tuple<std::deque<seqan3::dna4>, seqan3::simd::simd_type_t<uint16_t>>,
                                    std::tuple<std::deque<seqan3::dna4>, seqan3::simd::simd_type_t<uint32_t>>,
                                    std::tuple<std::deque<seqan3::dna4>, seqan3::simd::simd_type_t<uint64_t>>
                                   >;

TYPED_TEST_SUITE(view_to_simd_test, test_types, );

TEST(view_to_simd, concept_check)
{
    using cmp_type = std::vector<seqan3::dna4_vector>;
    using test_type = seqan3::detail::view_to_simd<seqan3::type_reduce_view<cmp_type &>,
                                                   seqan3::simd::simd_type_t<int8_t>>;

    using iter_t = decltype(std::ranges::begin(std::declval<test_type &>()));
    EXPECT_TRUE(std::input_iterator<iter_t>);

    EXPECT_EQ(std::ranges::input_range<cmp_type>, std::ranges::input_range<test_type>);
    EXPECT_NE(std::ranges::forward_range<cmp_type>, std::ranges::forward_range<test_type>);
    EXPECT_NE(std::ranges::bidirectional_range<cmp_type>, std::ranges::bidirectional_range<test_type>);
    EXPECT_NE(std::ranges::random_access_range<cmp_type>, std::ranges::random_access_range<test_type>);
    EXPECT_NE(std::ranges::random_access_range<cmp_type>, std::ranges::random_access_range<test_type>);

    EXPECT_EQ(std::ranges::range<cmp_type>, std::ranges::range<test_type>);
    EXPECT_NE(std::ranges::view<cmp_type>, std::ranges::view<test_type>);
    EXPECT_EQ(std::ranges::sized_range<cmp_type>, std::ranges::sized_range<test_type>);
    EXPECT_NE(std::ranges::common_range<cmp_type>, std::ranges::common_range<test_type>);
    EXPECT_NE(seqan3::const_iterable_range<cmp_type>, seqan3::const_iterable_range<test_type>);
    EXPECT_NE((std::ranges::output_range<cmp_type, seqan3::dna4_vector>),
              (std::ranges::output_range<test_type, seqan3::dna4_vector>));
}

TEST(view_to_simd, iter_concept)
{
    using cmp_type = std::vector<seqan3::dna4_vector>;
    using test_type = seqan3::detail::view_to_simd<seqan3::type_reduce_view<cmp_type &>,
                                                   seqan3::simd::simd_type_t<int8_t>>;
    using iter_t = std::ranges::iterator_t<test_type>;
    using sent_t = std::ranges::sentinel_t<test_type>;

    EXPECT_TRUE(std::input_or_output_iterator<iter_t>);
    EXPECT_TRUE(std::input_iterator<iter_t>);
    EXPECT_FALSE(std::forward_iterator<iter_t>);
    EXPECT_FALSE(std::bidirectional_iterator<iter_t>);
    EXPECT_FALSE(std::random_access_iterator<iter_t>);
    EXPECT_FALSE((std::output_iterator<iter_t, decltype(*std::declval<iter_t &>())>));
    EXPECT_TRUE((std::sentinel_for<sent_t, iter_t>));
}

TYPED_TEST(view_to_simd_test, size)
{
    typename TestFixture::view_to_simd_type to_simd_view{this->sequences};

    EXPECT_EQ(to_simd_view.size(), 64u);
}

TYPED_TEST(view_to_simd_test, empty)
{
    typename TestFixture::view_to_simd_type to_simd_view{this->sequences};

    EXPECT_EQ(to_simd_view.empty(), false);
}

TYPED_TEST(view_to_simd_test, iterate_without_padding)
{
    typename TestFixture::view_to_simd_type to_simd_view{this->sequences};
    this->compare(to_simd_view, this->transformed_simd_vec);
}

TYPED_TEST(view_to_simd_test, iterate_with_padding)
{
    typename TestFixture::view_to_simd_type to_simd_view{this->sequences, TestFixture::padding_value_custom};
    this->compare(to_simd_view, this->transformed_simd_vec_padded);
}

TYPED_TEST(view_to_simd_test, adaptor_pipe)
{
    using simd_t = typename TestFixture::simd_t;

    { // without padding
        auto v = this->sequences | seqan3::views::to_simd<simd_t>;
        this->compare(v, this->transformed_simd_vec);
    }

    { // w padding
        auto v = this->sequences | seqan3::views::to_simd<simd_t>(TestFixture::padding_value_custom);
        this->compare(v, this->transformed_simd_vec_padded);
    }

    { // w padding and calling range
        auto v = seqan3::views::to_simd<simd_t>(TestFixture::padding_value_custom)(this->sequences);
        this->compare(v, this->transformed_simd_vec_padded);
    }
}

TYPED_TEST(view_to_simd_test, adaptor_function)
{
    using simd_t = typename TestFixture::simd_t;

    { // without padding
        auto v = seqan3::views::to_simd<simd_t>(this->sequences);
        this->compare(v, this->transformed_simd_vec);
    }

    { // w padding
        auto v = seqan3::views::to_simd<simd_t>(this->sequences, TestFixture::padding_value_custom);
        this->compare(v, this->transformed_simd_vec_padded);
    }
}

TYPED_TEST(view_to_simd_test, empty_sequences)
{
    using simd_t = typename TestFixture::simd_t;
    std::vector<typename TestFixture::container_t> sequences;
    sequences.resize(seqan3::simd::simd_traits<simd_t>::length);

    auto v = sequences | seqan3::views::to_simd<simd_t>;
    this->compare(v, std::vector<simd_t, typename TestFixture::allocator_t>{});

    EXPECT_EQ(v.empty(), true);
    EXPECT_EQ(v.size(), 0u);
}

TYPED_TEST(view_to_simd_test, fewer_sequences)
{
    using simd_t = typename TestFixture::simd_t;
    this->sequences.pop_back();

    // delete the last sequence in the set.
    for (simd_t & vec : this->transformed_simd_vec)
        vec[seqan3::simd::simd_traits<simd_t>::length - 1] = TestFixture::padding_value_dna4;

    // If simd size is only 1, the compare range needs to be cleared.
    if (this->sequences.empty())
        this->transformed_simd_vec.clear();

    auto v = this->sequences | seqan3::views::to_simd<simd_t>;
    this->compare(v, this->transformed_simd_vec);

    if constexpr (seqan3::simd::simd_traits<simd_t>::length > 1)
    {
        EXPECT_EQ(v.empty(), false);
        EXPECT_EQ(v.size(), 64u);
    }
}

TYPED_TEST(view_to_simd_test, fewer_sequences_w_padding)
{
    using simd_t = typename TestFixture::simd_t;
    this->sequences.pop_back();

    for (simd_t & vec : this->transformed_simd_vec_padded)
        vec[seqan3::simd::simd_traits<simd_t>::length - 1] = TestFixture::padding_value_custom;

    // If simd size is only 1, the compare range needs to be cleared.
    if (this->sequences.empty())
        this->transformed_simd_vec_padded.clear();

    auto v = this->sequences | seqan3::views::to_simd<simd_t>(TestFixture::padding_value_custom);
    this->compare(v, this->transformed_simd_vec_padded);

    if constexpr (seqan3::simd::simd_traits<simd_t>::length > 1)
    {
        EXPECT_EQ(v.empty(), false);
        EXPECT_EQ(v.size(), 64u);
    }
}

TYPED_TEST(view_to_simd_test, empty_underlying_range)
{
    using simd_t = typename TestFixture::simd_t;
    std::vector<typename TestFixture::container_t> sequences{};

    auto v = sequences | seqan3::views::to_simd<simd_t>;
    this->compare(v, std::vector<simd_t, typename TestFixture::allocator_t>{});

    EXPECT_EQ(v.empty(), true);
    EXPECT_EQ(v.size(), 0u);
}

TYPED_TEST(view_to_simd_test, too_many_sequences)
{
    using seqan3::operator""_dna4;
    typename TestFixture::container_t cont;
    std::ranges::copy("ACGTACGACT"_dna4, std::cpp20::back_inserter(cont));
    this->sequences.push_back(cont);

    EXPECT_THROW(typename TestFixture::view_to_simd_type{this->sequences}, std::invalid_argument);
}

TYPED_TEST(view_to_simd_test, ends_not_on_chunk_boundary)
{
    using simd_t = typename TestFixture::simd_t;

    constexpr size_t seq1_size = 10;
    // modify the sequence to get a size that is not a multiple of simd length.
    this->sequences[0].resize(seq1_size);

    // Second longest sequence in the set now.
    size_t new_max_length = TestFixture::max_sequence_length - seqan3::simd::simd_traits<simd_t>::length - 1;

    // If simd size is only 1, the compare range only holds one sequence which must have the same size.
    if (this->sequences.size() == 1)
        new_max_length = seq1_size;

    // First update the test vectors padding values
    for (size_t i = seq1_size; i < new_max_length; ++i)
        this->transformed_simd_vec[i][0] = this->padding_value_dna4;

    // Second shrink test vector to second longest sequence.
    this->transformed_simd_vec.resize(new_max_length);

    // Now test against the test vector.
    auto simd_view = this->sequences | seqan3::views::to_simd<simd_t>;
    this->compare(simd_view, this->transformed_simd_vec);
}

// See https://github.com/seqan/seqan3/pull/1813
// Before this fix we created a default constructed instance of the underlying range to use it as an empty range.
// But a default constructed view is not guaranteed to be comparable, i.e. it results in UB.
// This test checks now that if the underlying range is a view the conversion to simd sequence still works.
TYPED_TEST(view_to_simd_test, issue_1813)
{
    using simd_t = typename TestFixture::simd_t;
    using container_t = typename TestFixture::container_t;
    using take_view_t = decltype(std::declval<container_t &>() | std::views::take(5));

    std::vector<take_view_t> take_sequences{};

    for (auto & sequence : this->sequences)
        take_sequences.push_back(sequence | std::views::take(10));

    // Remove one sequence
    take_sequences.pop_back();

    // If simd size is only 1, the compare range needs to be cleared.
    if (take_sequences.empty())
        this->transformed_simd_vec.clear();

    // delete the last sequence in the set.
    for (simd_t & vec : this->transformed_simd_vec)
        vec[seqan3::simd::simd_traits<simd_t>::length - 1] = TestFixture::padding_value_dna4;

    { // without padding
        auto v = seqan3::views::to_simd<simd_t>(take_sequences);
        this->compare(v, this->transformed_simd_vec | std::views::take(10));
    }
}

// https://github.com/seqan/seqan3/issues/1941
TYPED_TEST(view_to_simd_test, issue_1941)
{
    using simd_t = typename TestFixture::simd_t;
    using view_t = decltype(this->sequences | seqan3::views::to_simd<simd_t>);

    using value_t = std::ranges::range_value_t<view_t>;
    using reference_t = std::ranges::range_reference_t<view_t>;

    EXPECT_TRUE((std::common_with<value_t, reference_t>));
}