// ==========================================================================
//                 SeqAn - The Library for Sequence Analysis
// ==========================================================================
// Copyright (c) 2006-2026, Knut Reinert, FU Berlin
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// ==========================================================================
// Author: Rene Rahn <rene.rahn@fu-berlin.de>
// ==========================================================================

#ifndef TESTS_ALIGN_TEST_ALIGN_SIMD_BASE_H_
#define TESTS_ALIGN_TEST_ALIGN_SIMD_BASE_H_

#include <tuple>

#include <seqan/basic.h>
#include <seqan/align.h>

#include "test_mock.h"

// ----------------------------------------------------------------------------
// Class SimdAlignTest
// ----------------------------------------------------------------------------

// Common test class instance, which stores the types to be accessed.
template <typename TTuple>
class SimdAlignTest : public seqan2::Test
{
public:
    using TAlignConfig = std::tuple_element_t<0, TTuple>;
    using TLengthParam = std::tuple_element_t<1, TTuple>;
    using TBandSwitch = std::tuple_element_t<2, TTuple>;
};

namespace impl
{
namespace test_align_simd
{

struct LocalAlignTester_
{
    template <typename TAlign,
              typename TScoreValue, typename TScoreSpec,
              typename TConfig>
    static auto
    run(TAlign & align,
        seqan2::Score<TScoreValue, TScoreSpec> const & score,
        TConfig const &,
        int const lDiag,
        int const uDiag)
    {
        if (lDiag == std::numeric_limits<int>::min() && uDiag == std::numeric_limits<int>::max())
            return localAlignment(align, score);
        else
            return localAlignment(align, score, lDiag, uDiag);
    }
};

struct GlobalAlignTester_
{
    template <typename TAlign,
              typename TScoreValue, typename TScoreSpec,
              typename TConfig>
    static auto
    run(TAlign & align,
        seqan2::Score<TScoreValue, TScoreSpec> const & score,
        TConfig const & config,
        int const lDiag,
        int const uDiag)
    {
        if (lDiag == std::numeric_limits<int>::min() && uDiag == std::numeric_limits<int>::max())
            return globalAlignment(align, score, config);
        else
            return globalAlignment(align, score, config, lDiag, uDiag);
    }
};

struct GlobalAlignScoreTester_
{
    template <typename TStringsH,
              typename TStringsV,
              typename TScoreValue, typename TScoreSpec,
              typename TConfig>
    static auto
    run(TStringsH const & strH,
        TStringsV const & strV,
        seqan2::Score<TScoreValue, TScoreSpec> const & score,
        TConfig const & config,
        int const lDiag,
        int const uDiag)
    {
        if (lDiag == std::numeric_limits<int>::min() && uDiag == std::numeric_limits<int>::max())
            return globalAlignmentScore(strH, strV, score, config);
        else
            return globalAlignmentScore(strH, strV, score, config, lDiag, uDiag);
    }
};

struct LocalScoreTester_
{
    template <typename TStringsH,
              typename TStringsV,
              typename TScoreValue, typename TScoreSpec,
              typename TConfig>
    static auto
    run(TStringsH const & strH,
        TStringsV const & strV,
        seqan2::Score<TScoreValue, TScoreSpec> const & score,
        TConfig const & /*config*/,
        int const lDiag,
        int const uDiag)
    {
        if (lDiag == seqan2::MinValue<int>::VALUE && uDiag == seqan2::MaxValue<int>::VALUE)
            return localAlignmentScore(strH, strV, score);
        else
            return localAlignmentScore(strH, strV, score, lDiag, uDiag);
    }
};
}  // namespace test_align_simd
}  // namespace impl

// ----------------------------------------------------------------------------
// Function testAlignSimd()
// ----------------------------------------------------------------------------

template <typename TAlphabet,
          typename TFunctor,
          typename TScoreValue, typename TScoreSpec,
          typename TAlignConfig,
          typename TSimdLength>
void testAlignSimd(TFunctor const &,
                   seqan2::Score<TScoreValue, TScoreSpec> const & score,
                   TAlignConfig const & config,
                   TSimdLength const & /*tag*/,
                   int const lDiag = std::numeric_limits<int>::min(),
                   int const uDiag = std::numeric_limits<int>::max())
{
    auto sets = impl::test_align_mock::TestSequences_<TAlphabet, TSimdLength>::getSequences();

    // Prepare an align object with the sequences.
    seqan2::StringSet<seqan2::Align<seqan2::String<TAlphabet> > > alignments;
    resize(alignments, length(std::get<0>(sets)));
    auto zipCont = makeZipView(alignments, std::get<0>(sets), std::get<1>(sets));

    for (auto tuple : zipCont)
    {
        resize(rows(std::get<0>(tuple)), 2);
        assignSource(row(std::get<0>(tuple), 0), std::get<1>(tuple));
        assignSource(row(std::get<0>(tuple), 1), std::get<2>(tuple));
    }

    // Run the SIMD accelerated alignment.
    seqan2::String<TScoreValue> scores = TFunctor::run(alignments, score, config, lDiag, uDiag);
    SEQAN_ASSERT_EQ(length(scores), length(alignments));

    // Check correctness of alignments using sequential alignment.
    // NOTE(rrahn): There seems to be a bug with the intel compiler and the zipView.
    // The following works without running into the problem, but we need to investigate the issue at some point.
    auto itBeg = makeZipIterator(begin(scores, seqan2::Standard()), begin(alignments, seqan2::Standard()));
    auto itEnd = makeZipIterator(end(scores, seqan2::Standard()), end(alignments, seqan2::Standard()));

    for (auto it = itBeg; it != itEnd; ++it)
    {
        auto res = *it;
        typename std::decay<decltype(std::get<1>(res))>::type goldAlign;
        resize(rows(goldAlign), 2);
        assignSource(row(goldAlign, 0), source(row(std::get<1>(res), 0)));
        assignSource(row(goldAlign, 1), source(row(std::get<1>(res), 1)));

        TScoreValue goldScore = TFunctor::run(goldAlign, score, config, lDiag, uDiag);

        SEQAN_ASSERT_EQ(std::get<0>(res), goldScore);
        SEQAN_ASSERT(row(std::get<1>(res), 0) == row(goldAlign, 0));
        SEQAN_ASSERT(row(std::get<1>(res), 1) == row(goldAlign, 1));
    }
}

// Helper function to set band parameters.
template <typename TAlphabet,
          typename TFunctor,
          typename TScoreValue, typename TScoreSpec,
          typename TAlignConfig,
          typename TSimdLength,
          typename TBandFlag>
void testAlignSimd(TFunctor const &,
                   seqan2::Score<TScoreValue, TScoreSpec> const & score,
                   TAlignConfig const & config,
                   TSimdLength const & /*tag*/,
                   TBandFlag const &)
{
    if (seqan2::IsSameType<TBandFlag, seqan2::BandOff>::VALUE)
        testAlignSimd<TAlphabet>(TFunctor(), score, config, TSimdLength());
    else
        testAlignSimd<TAlphabet>(TFunctor(), score, config, TSimdLength(), -4, 6);
}

// ----------------------------------------------------------------------------
// Function testAlignScoreSimd()
// ----------------------------------------------------------------------------

template <typename TAlphabet,
          typename TTester,
          typename TScoreValue, typename TScoreSpec,
          typename TAlignConfig,
          typename TSimdLength>
void testAlignSimdScore(TTester const &,
                        seqan2::Score<TScoreValue, TScoreSpec> const & score,
                        TAlignConfig const & config,
                        TSimdLength const & /*tag*/,
                        int const lDiag = std::numeric_limits<int>::min(),
                        int const uDiag = std::numeric_limits<int>::max())
{
    auto sets = impl::test_align_mock::TestSequences_<TAlphabet, TSimdLength>::getSequences();

    seqan2::String<TScoreValue> scores = TTester::run(std::get<0>(sets), std::get<1>(sets), score, config, lDiag, uDiag);

    SEQAN_ASSERT_EQ(length(scores), length(std::get<0>(sets)));

    auto zipRes = makeZipView(scores, std::get<0>(sets), std::get<1>(sets));
    for (auto res : zipRes)
    {
        TScoreValue goldScore = TTester::run(std::get<1>(res), std::get<2>(res), score, config, lDiag, uDiag);
        SEQAN_ASSERT_EQ(std::get<0>(res), goldScore);
    }
}

// Helper function to set band parameters.
template <typename TAlphabet,
          typename TFunctor,
          typename TScoreValue, typename TScoreSpec,
          typename TAlignConfig,
          typename TSimdLength,
          typename TBandFlag>
void testAlignSimdScore(TFunctor const &,
                        seqan2::Score<TScoreValue, TScoreSpec> const & score,
                        TAlignConfig const & config,
                        TSimdLength const & /*tag*/,
                        TBandFlag const &)
{
    if (seqan2::IsSameType<TBandFlag, seqan2::BandOff>::VALUE)
        testAlignSimdScore<TAlphabet>(TFunctor(), score, config, TSimdLength());
    else
        testAlignSimdScore<TAlphabet>(TFunctor(), score, config, TSimdLength(), -4, 6);
}

#endif  // #ifndef TESTS_ALIGN_TEST_ALIGN_SIMD_BASE_H_
