// ==========================================================================
//                 SeqAn - The Library for Sequence Analysis
// ==========================================================================
// Copyright (c) 2006-2026, Knut Reinert, FU Berlin
// All rights reserved.
//
// Redistribution and use in source and binary forms, with or without
// modification, are permitted provided that the following conditions are met:
//
//     * Redistributions of source code must retain the above copyright
//       notice, this list of conditions and the following disclaimer.
//     * Redistributions in binary form must reproduce the above copyright
//       notice, this list of conditions and the following disclaimer in the
//       documentation and/or other materials provided with the distribution.
//     * Neither the name of Knut Reinert or the FU Berlin nor the names of
//       its contributors may be used to endorse or promote products derived
//       from this software without specific prior written permission.
//
// THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
// AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
// IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
// ARE DISCLAIMED. IN NO EVENT SHALL KNUT REINERT OR THE FU BERLIN BE LIABLE
// FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
// DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
// SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
// CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT
// LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY
// OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH
// DAMAGE.
//
// ==========================================================================
// Author: David Weese <david.weese@fu-berlin.de>
// ==========================================================================

#ifndef SEQAN_HEADER_INDEX_QGRAM_OPENADRESSING_H
#define SEQAN_HEADER_INDEX_QGRAM_OPENADRESSING_H

namespace seqan2
{

    struct OpenAddressing_;
    typedef Tag<OpenAddressing_> OpenAddressing;

    template <typename THashValue>
    struct BucketMap
    {
        static const THashValue EMPTY;
        String<THashValue> qgramCode;
    };

    template <typename THashValue>
    const THashValue BucketMap<THashValue>::EMPTY = (THashValue)-1;

    // use the index value type as shape value type
    template < typename TObject, typename TShapeSpec >
    struct Fibre< Index<TObject, IndexQGram<TShapeSpec, OpenAddressing> >, FibreBucketMap>
    {
        typedef typename Fibre< Index<TObject, IndexQGram<TShapeSpec, OpenAddressing> >, FibreShape>::Type TShape;
        typedef typename Value<TShape>::Type    THashValue;
        typedef BucketMap<THashValue>            Type;
    };

/*!
 * @class OpenAddressingQGramIndex
 * @extends IndexQGram
 * @headerfile <seqan/index.h>
 * @brief A <i>q</i>-gram that uses open addressing hashing instead of an array.
 *
 * @signature template <typename TIndex, typename TShapeSpec>
 *            class Index<TText, IndexQGram<TShapeSpec, OpenAddressing> >;
 *
 * @tparam TText      The @link TextConcept text type @endlink.
 * @tparam TShapeSpec The @link Shape @endlink specialization type.
 *
 * This index uses a non-trivial hashing for mapping q-gram hash values to buckets.  This reduces the sizes of bucket
 * directories (QGramDir, QGramCountsDir fibres) from &Sigma;<i><sup>q</sup></i> to min(<i>&alpha; &middot; n</i>,
 * \Sigma<i><sup>q</sup></i>), for a load factor <i>&alpha; &gt; 1</i>.  A bucket still stores occurrences (or counts)
 * of the same <i>q</i>-gram, but in contrast to the @link IndexQGram @endlink index, buckets are in random order due to
 * the hashing.
 *
 * @var double OpenAddressingQGramIndex::alpha
 * @brief Load factor.  Controls space/time-tradeoff and must be greater 1.  Default value is 1.6.
 */

    template < typename TObject, typename TShapeSpec >
    class Index<TObject, IndexQGram<TShapeSpec, OpenAddressing> >
    {
    private:
        static const double defaultAlpha;
    public:
        typedef typename Member<Index, QGramText>::Type     TTextMember;
        typedef typename Fibre<Index, QGramText>::Type        TText;
        typedef typename Fibre<Index, QGramSA>::Type        TSA;
        typedef typename Fibre<Index, QGramDir>::Type        TDir;
        typedef typename Fibre<Index, QGramCounts>::Type    TCounts;
        typedef typename Fibre<Index, QGramCountsDir>::Type    TCountsDir;
        typedef typename Fibre<Index, QGramShape>::Type        TShape;
        typedef typename Fibre<Index, QGramBucketMap>::Type    TBucketMap;
        typedef typename Cargo<Index>::Type                    TCargo;
        typedef typename Size<Index>::Type                    TSize;

        static_assert(WEIGHT<TShape>::VALUE <= 31, "Incompatible q-gram size. Must be in range [1, 31].");

        TTextMember     text;        // underlying text
        TSA                sa;            // suffix array sorted by the first q chars
        TDir            dir;        // bucket directory
        TCounts            counts;        // counts each q-gram per sequence
        TCountsDir        countsDir;    // directory for count buckets
        TShape            shape;        // underlying shape
        TCargo            cargo;        // user-defined cargo
        TBucketMap        bucketMap;    // bucketMap table (used by open-addressing index)
        TSize            stepSize{1};   // store every <stepSize>'th q-gram in the index

        double            alpha;        // for m entries the hash map has at least size alpha*m

        /*!
         * @fn OpenAddressingQGramIndex::Index
         * @brief Constructor
         *
         * @signature Index::Index();
         * @signature Index::Index(index);
         * @signature Index::Index(text[, shape]);
         *
         * @param[in] index Other Index object to copy from.
         * @param[in] text  The text to be indexed.
         * @param[in] shape The qgram @link Shape @endlink to be applied.
         */

        Index():
            stepSize(1),
            alpha(defaultAlpha) {}

        Index(Index const & other):
            text(other.text),
            sa(other.sa),
            dir(other.dir),
            counts(other.counts),
            countsDir(other.countsDir),
            shape(other.shape),
            cargo(other.cargo),
            bucketMap(other.bucketMap),
            stepSize(1),
            alpha(defaultAlpha) {}

        Index & operator=(Index const &) = default;

        template <typename TText_>
        Index(TText_ &_text):
            text(_text),
            stepSize(1),
            alpha(defaultAlpha) {}

        template <typename TText_>
        Index(TText_ const &_text):
            text(_text),
            stepSize(1),
            alpha(defaultAlpha) {}

        template <typename TText_, typename TShape_>
        Index(TText_ &_text, TShape_ const &_shape):
            text(_text),
            shape(_shape),
            stepSize(1),
            alpha(defaultAlpha)
            {
                if (weight(_shape) > 31u)
                    throw std::runtime_error("Incompatible q-gram size. Must be in range [1, 31].");
            }

        template <typename TText_, typename TShape_>
        Index(TText_ const &_text, TShape_ const &_shape):
            text(_text),
            shape(_shape),
            stepSize(1),
            alpha(defaultAlpha)
            {
                if (weight(_shape) > 31u)
                    throw std::runtime_error("Incompatible q-gram size. Must be in range [1, 31].");
            }
    };


    template < typename TObject, typename TShapeSpec >
    const double Index<TObject, IndexQGram<TShapeSpec, OpenAddressing> >::defaultAlpha = 1.6;

    //////////////////////////////////////////////////////////////////////////////
    // Counting sort - Step 1: Clear directory
    template < typename TDir, typename THashValue, typename TParallelTag >
    inline void _qgramClearDir(TDir &dir, BucketMap<THashValue> &bucketMap, Tag<TParallelTag> parallelTag)
    {
        typedef BucketMap<THashValue> TBucketMap;
        if (!empty(dir))
            arrayFill(begin(dir, Standard()), end(dir, Standard()), 0, parallelTag);
        if (!empty(bucketMap.qgramCode))
            arrayFill(begin(bucketMap.qgramCode, Standard()), end(bucketMap.qgramCode, Standard()), TBucketMap::EMPTY, parallelTag);
    }

    template < typename TBucketMap, typename TValue >
    inline TValue
    _hashFunction(TBucketMap const &, TValue val)
    {
        // WARNING:
        // As SSE4.2 is not always available, the bucket order is platform dependent
#ifdef __SSE4_2__
        return _mm_crc32_u64(0ul, val);
#else
        return ((val * 43) ^ (val >> 20)) + val;
#endif
    }

    template < typename THashValue, typename THashValue2, typename TParallelTag >
    inline THashValue
    requestBucket(BucketMap<THashValue> &bucketMap, THashValue2 code, Tag<TParallelTag> parallelTag)
    {
        typedef BucketMap<THashValue> TBucketMap;
        typedef unsigned long TSize;
        // get size of the index

        // check whether bucket map is disabled and
        // where the hash should be found if no collision took place before
        TSize hlen = length(bucketMap.qgramCode);
        if (hlen == 0ul) return code;

        TSize h1 = _hashFunction(bucketMap, code);
#ifdef SEQAN_OPENADDRESSING_COMPACT
        --hlen;
        h1 %= hlen;
#else
        hlen -= 2;
        h1 &= hlen;
#endif
        // was the entry empty or occupied by our code?
        THashValue currentCode = atomicCas(bucketMap.qgramCode[h1], TBucketMap::EMPTY, code, parallelTag);
        if (currentCode == TBucketMap::EMPTY || currentCode == code)
            return h1;

        // if not we have a collision -> probe for our code or an empty entry
        //
        // do linear probing if we need to save memory (when SEQAN_OPENADDRESSING_COMPACT is defined)
        // otherwise do quadratic probing to avoid clustering (Cormen 1998)
        TSize delta = 0;
        (void)delta;
        do {
#ifdef SEQAN_OPENADDRESSING_COMPACT
            h1 = (h1 + 1) % hlen;               // linear probing guarantees that all entries are visited
#else
            h1 = (h1 + delta + 1) & hlen;       // for power2-sized tables the (i*i+i)/2 probing guarantees the same
            ++delta;
#endif
            currentCode = atomicCas(bucketMap.qgramCode[h1], TBucketMap::EMPTY, code, parallelTag);
        } while (currentCode != TBucketMap::EMPTY && currentCode != code);
        return h1;
    }

    template < typename THashValue, typename THashValue2 >
    inline THashValue
    getBucket(BucketMap<THashValue> const &bucketMap, THashValue2 code)
    {
        typedef BucketMap<THashValue> TBucketMap;
        typedef unsigned long TSize;
        // get size of the index

        // check whether bucket map is disabled and
        // where the hash should be found if no collision took place before
        TSize hlen = length(bucketMap.qgramCode);
        if (hlen == 0ul) return code;

        TSize h1 = _hashFunction(bucketMap, code);
#ifdef SEQAN_OPENADDRESSING_COMPACT
        --hlen;
        h1 %= hlen;
#else
        hlen -= 2;
        h1 &= hlen;
#endif

        // probe for our code or an empty entry
        //
        // do linear probing if we need to save memory (when SEQAN_OPENADDRESSING_COMPACT is defined)
        // otherwise do quadratic probing to avoid clustering (Cormen 1998)
        TSize delta = 0;
        (void)delta;
        while (bucketMap.qgramCode[h1] != code && bucketMap.qgramCode[h1] != TBucketMap::EMPTY)
        {
#ifdef SEQAN_OPENADDRESSING_COMPACT
            h1 = (h1 + 1) % hlen;               // linear probing guarantees that all entries are visited
#else
            h1 = (h1 + delta + 1) & hlen;       // for power2-sized tables the (i*i+i)/2 probing guarantees the same
            ++delta;
#endif
        }
        return h1;
    }

    template <typename TBucketMap>
    inline bool _emptyBucketMap(TBucketMap const &bucketMap)
    {
        return empty(bucketMap);
    }

    inline bool _emptyBucketMap(Nothing const &)
    {
        return false;
    }

    template <typename TObject, typename TShapeSpec>
    inline int64_t _fullDirLength(Index<TObject, IndexQGram<TShapeSpec, OpenAddressing> > const &index)
    {
        typedef Index<TObject, IndexQGram<TShapeSpec, OpenAddressing> >    TIndex;
        typedef typename Fibre<TIndex, QGramDir>::Type                        TDir;
        typedef typename Fibre<TIndex, FibreShape>::Type                    TShape;
        typedef typename Host<TShape>::Type                                    TTextValue;
        typedef typename Value<TDir>::Type                                    TDirValue;
        typedef typename Value<TShape>::Type                                THashValue;

        double num_qgrams = _qgramQGramCount(index) * index.alpha;
        double max_qgrams = pow((double)ValueSize<TTextValue>::VALUE, (double)weight(indexShape(index)));
        int64_t qgrams;

        // compare size of open adressing with 1-1 mapping and use the smaller one
        if (num_qgrams * (sizeof(TDirValue) + sizeof(THashValue)) < max_qgrams * sizeof(TDirValue))
        {
            qgrams = (int64_t)ceil(num_qgrams);
#ifndef SEQAN_OPENADDRESSING_COMPACT
            int64_t power2 = 1;
            while (power2 < qgrams)
                power2 <<= 1;
            qgrams = power2;
#endif
            resize(const_cast<TIndex &>(index).bucketMap.qgramCode, qgrams + 1, Exact());
        } else
        {
            qgrams = (int64_t)ceil(max_qgrams);
            clear(const_cast<TIndex &>(index).bucketMap.qgramCode);    // 1-1 mapping, no bucket map needed
        }

        return qgrams + 1;
    }

// ----------------------------------------------------------------------------
// Function open()
// ----------------------------------------------------------------------------

template < typename TText, typename TShapeSpec>
inline bool open(Index<TText, IndexQGram<TShapeSpec, OpenAddressing> > &index, const char *fileName, int openMode)
{
    String<char> name;

    name = fileName;    append(name, ".txt");
    if (!open(getFibre(index, QGramText()), toCString(name), openMode)) return false;

    name = fileName;    append(name, ".sa");
    if (!open(getFibre(index, QGramSA()), toCString(name), openMode)) return false;

    name = fileName;    append(name, ".dir");
    if (!open(getFibre(index, QGramDir()), toCString(name), openMode)) return false;

    name = fileName;    append(name, ".bkt");
    if (!open(getFibre(index, QGramBucketMap()).qgramCode, toCString(name), openMode)) return false;

    return true;
}

template <typename TText, typename TShapeSpec>
inline bool open(Index<TText, IndexQGram<TShapeSpec, OpenAddressing> > &index, const char *fileName)
{
    return open(index, fileName, OPEN_RDONLY);
}

// ----------------------------------------------------------------------------
// Function save()
// ----------------------------------------------------------------------------

template <typename TText, typename TShapeSpec>
inline bool save(Index<TText, IndexQGram<TShapeSpec, OpenAddressing> > &index, const char *fileName, int openMode)
{
    String<char> name;

    name = fileName;    append(name, ".txt");
    if (!save(getFibre(index, QGramText()), toCString(name), openMode)) return false;

    name = fileName;    append(name, ".sa");
    if (!save(getFibre(index, QGramSA()), toCString(name), openMode)) return false;

    name = fileName;    append(name, ".dir");
    if (!save(getFibre(index, QGramDir()), toCString(name), openMode)) return false;

    name = fileName;    append(name, ".bkt");
    if (!save(getFibre(index, QGramBucketMap()).qgramCode, toCString(name), openMode)) return false;

    return true;
}

template <typename TText, typename TShapeSpec>
inline bool save(Index<TText, IndexQGram<TShapeSpec, OpenAddressing> > &index, const char *fileName)
{
    return save(index, fileName, OPEN_WRONLY | OPEN_CREATE);
}

}

#endif //#ifndef SEQAN_HEADER_...
