// ==========================================================================
//                 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
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// 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_LCP_H
#define SEQAN_HEADER_INDEX_LCP_H

namespace seqan2
{

//namespace seqan2_NAMESPACE_PIPELINING
//{

    struct Kasai {};
    struct KasaiOriginal {};    // original, but more space-consuming algorithm


    //////////////////////////////////////////////////////////////////////////////
    // external LCP algorithm (modified Kasai et al. for pipelining)
    //////////////////////////////////////////////////////////////////////////////


    template < typename TTextInput, typename TSuffixArrayInput >
    struct Value< Pipe< Bundle2< TTextInput, TSuffixArrayInput >, Kasai > > {
        typedef typename Size<TTextInput>::Type Type;
    };

    template <typename InType, typename Result = typename Value< typename Value<InType, 2>::Type>::Type>
    struct _mapInverse : public std::function<Result(InType)> {
        inline Result operator()(const InType& x) const
        { return x.i2[0]; }
    };

    //////////////////////////////////////////////////////////////////////////////
    // lcp class
    template < typename TTextInput, typename TSuffixArrayInput >
    struct Pipe< Bundle2< TTextInput, TSuffixArrayInput >, Kasai >
    {
        // *** SPECIALIZATION ***

        typedef Pipe< TSuffixArrayInput, Echoer<2,false> > TEchoer;
                                        typedef _mapInverse<TypeOf_(TEchoer)> map_inverse_t;
                                        typedef typename Size<TTextInput>::Type    TSize;
        typedef Pool< TypeOf_(TEchoer), MapperSpec< MapperConfigSize< map_inverse_t, TSize> > > TInverter;
                                        typedef Pair<TSize> TCoreType;
        typedef Pool< TCoreType, MapperSpec< MapperConfigSize< filterI1<TCoreType>, TSize > > > TLinearMapper;
        typedef Pipe< TLinearMapper, Filter< filterI2<TCoreType> > > TFilter;

        TTextInput                *textIn;
        TSuffixArrayInput        *suffixArrayIn;
        TLinearMapper           mapper;
        TFilter                    in;
        const LcpConfig            conf;

        Pipe():
            in(mapper) {}

        Pipe(const LcpConfig &_conf):
            in(mapper),
            conf(_conf) {}

        Pipe(Bundle2< TTextInput, TSuffixArrayInput > const &_bundleIn):
            textIn(&_bundleIn.in1),
            suffixArrayIn(&_bundleIn.in2),
            in(mapper)
        {
            process();
        }

        Pipe(Bundle2< TTextInput, TSuffixArrayInput > const &_bundleIn, LcpConfig const &_conf):
            textIn(&_bundleIn.in1),
            suffixArrayIn(&_bundleIn.in2),
            in(mapper),
            conf(_conf)
        {
            process();
        }

        inline void process() {
            process(*textIn, *suffixArrayIn);
        }

        template < typename TTextInput_, typename TSuffixArrayInput_ >
        bool process(TTextInput_ &textIn, TSuffixArrayInput_ &suffixArrayIn) {

            // *** INSTANTIATION ***

            TEchoer                        echoer(suffixArrayIn);
            TInverter                    inverter(echoer);

            #ifdef SEQAN_DEBUG_INDEX
                std::cerr << "--- CREATE LCP TABLE ---" << std::endl;
                std::cerr << "Start Kasai [pipelining]" << std::endl;
                std::cerr << "  invert suffix array" << std::endl;
            #endif
            inverter << echoer;
            SEQAN_PROMARK("Suffix-Array invertiert");

            _lcpProcess(textIn, inverter, mapper);
            return true;
        }

        inline typename Value<Pipe>::Type const operator*() const {
            return *in;
        }

        inline Pipe& operator++() {
            ++in;
            return *this;
        }
    };

    // not sure which interface is more intuitive, we support both
    // you can call "skew << pipe" or "skew_t skew(pipe); skew.process()"
    // for the first we would need no _in member
    template < typename TInput, typename TTextInput_, typename TSuffixArrayInput_ >
    inline bool operator<<(Pipe< TInput, Kasai > &me, Bundle2< TTextInput_, TSuffixArrayInput_ > const &bundleIn) {
         return me.process(bundleIn.in1, bundleIn.in2);
    }



    //////////////////////////////////////////////////////////////////////////////
    // external LCP algorithm (optimized for multiple sequences)
    //////////////////////////////////////////////////////////////////////////////


    template < typename TTextInput, typename TSuffixArrayInput, typename TPair, typename TLimitsString >
    struct Value< Pipe< Bundle2< TTextInput, TSuffixArrayInput >, Multi<Kasai, TPair, TLimitsString> > > {
        typedef typename Value<TLimitsString>::Type Type;
    };

    template <typename InType, typename TLimitsString, typename Result = typename Value<TLimitsString>::Type>
    struct _mapInverseMulti : public std::function<Result(InType)> {
        TLimitsString const &limits;
        _mapInverseMulti(TLimitsString const &_limits) : limits(_limits) {}
        inline Result operator()(const InType& x) const
        {
            return posGlobalize(x.i2[0], limits);
        }
    };

    //////////////////////////////////////////////////////////////////////////////
    // lcp class
    template < typename TTextInput, typename TSuffixArrayInput, typename TPair, typename TLimitsString >
    struct Pipe< Bundle2< TTextInput, TSuffixArrayInput >, Multi<Kasai, TPair, TLimitsString> >
    {
        // *** SPECIALIZATION ***

        typedef Pipe< TSuffixArrayInput, Echoer<2,false> > TEchoer;
                                        typedef _mapInverseMulti<TypeOf_(TEchoer), TLimitsString, TSizeOf_(TEchoer)> map_inverse_t;
                                        typedef typename Size<TTextInput>::Type    TSize;
        typedef Pool< TypeOf_(TEchoer), MapperSpec< MapperConfigSize< map_inverse_t, TSize> > > TInverter;
                                        typedef Pair<TSize> TCoreType;
        typedef Pool< TCoreType, MapperSpec< MapperConfigSize< filterI1<TCoreType>, TSize > > > TLinearMapper;
        typedef Pipe< TLinearMapper, Filter< filterI2<TCoreType> > > TFilter;

        TLinearMapper           mapper;
        TFilter                    in;
        TLimitsString const        &limits;
        const LcpConfig            conf;

        Pipe(TLimitsString const &_limits):
            in(mapper),
            limits(_limits)    {}

        Pipe(TLimitsString const &_limits, LcpConfig const &_conf):
            in(mapper),
            limits(_limits),
            conf(_conf) {}

        Pipe(Bundle2< TTextInput, TSuffixArrayInput > const &_bundleIn, TLimitsString const &_limits):
            in(mapper),
            limits(_limits)
        {
            process(_bundleIn.in1, _bundleIn.in2);
        }

        Pipe(Bundle2< TTextInput, TSuffixArrayInput > const &_bundleIn, TLimitsString const &_limits, LcpConfig const &_conf):
            in(mapper),
            limits(_limits),
            conf(_conf)
        {
            process(_bundleIn.in1, _bundleIn.in2);
        }

        template < typename TTextInput_, typename TSuffixArrayInput_ >
        bool process(TTextInput_ &textIn, TSuffixArrayInput_ &suffixArrayIn) {

            // *** INSTANTIATION ***

            TEchoer                        echoer(suffixArrayIn);
            map_inverse_t                _mapInverse(limits);
            TInverter                    inverter(echoer, _mapInverse);

            #ifdef SEQAN_DEBUG_INDEX
                std::cerr << "--- CREATE LCP TABLE ---" << std::endl;
                std::cerr << "Start Kasai [pipelining,stringset]" << std::endl;
                std::cerr << "  invert suffix array" << std::endl;
            #endif
            inverter << echoer;
            SEQAN_PROMARK("Suffix-Array invertiert");

            _lcpProcessMulti(textIn, limits, inverter, mapper);
            return true;
        }

        inline typename Value<Pipe>::Type const operator*() const {
            return *in;
        }

        inline Pipe& operator++() {
            ++in;
            return *this;
        }
    };

    // not sure which interface is more intuitive, we support both
    // you can call "skew << pipe" or "skew_t skew(pipe); skew.process()"
    // for the first we would need no _in member
    template < typename TInput, typename TTextInput_, typename TSuffixArrayInput_, typename TPair, typename TLimitsString >
    inline bool operator<<(Pipe< TInput, Multi<Kasai, TPair, TLimitsString> > &me, Bundle2< TTextInput_, TSuffixArrayInput_ > const &bundleIn) {
         return me.process(bundleIn.in1, bundleIn.in2);
    }



    //////////////////////////////////////////////////////////////////////////////
    // internal Kasai algorithm
    //////////////////////////////////////////////////////////////////////////////

    template <
        typename TLCP,
        typename TText,
        typename TSA >
    struct LcpCreatorRandomAccess_<TLCP, TText, TSA, Kasai>
    {
        typedef typename AllowsFastRandomAccess<TLCP>::Type  TRandomLCP;
        typedef typename AllowsFastRandomAccess<TSA>::Type   TRandomSA;
        typedef typename And<TRandomLCP, TRandomSA>::Type Type;
    };


    template < typename TLCPTable,
               typename TText,
               typename TSA >
    void _createLCPTableRandomAccess(
        TLCPTable &LCP,
        TText const &s,
        TSA const &SA,
        KasaiOriginal const)
    {
        typedef typename Value<TSA>::Type TSize;

        #ifdef SEQAN_DEBUG_INDEX
            std::cerr << "--- CREATE LCP TABLE ---" << std::endl;
            std::cerr << "Start Kasai [random access]" << std::endl;
            if (sizeof(TSize) > 4)
                std::cerr << "WARNING: TSize size is greater 4 (Kasai)" << std::endl;
        #endif

        TSize n = length(s);
        if (n == 0) return;

        #ifdef SEQAN_DEBUG_INDEX
            TSize lcpMax = 0, lcpAvrg = 0, lcpNumer = 0, sigma = 1;    // for lcpMax, lcpMean, |Sigma|
        #endif

        String<TSize, Alloc<> > ISA;
        resize(ISA, n, Exact());

        for(TSize i = 0; i < n; ++i)
            ISA[SA[i]] = i;

        SEQAN_PROMARK("Suffix-Array invertiert");

        typename Iterator<TText const>::Type Ibegin = begin(s);
        typename Iterator<TText const>::Type I = Ibegin, J;
        for(TSize i = 0, h = 0, j, isa; i < n; ++i) {
            if ((isa = ISA[i])) {
                J = Ibegin + h + (j = SA[isa - 1]);
                for(TSize hMax = _min(n - i, n - j); h < hMax && *I == *J; ++I, ++J, ++h) ;
                LCP[isa - 1] = h;
                #ifdef SEQAN_DEBUG_INDEX
                    if ((lcpNumer += h) > n) {
                        lcpNumer -= n;
                        ++lcpAvrg;
                    }
                    if (lcpMax < h) lcpMax = h;
                    if (!h) ++sigma;
                #endif
            }
            if (h) --h;
            else ++I;
        }
        LCP[n - 1] = 0;
        #ifdef SEQAN_DEBUG_INDEX
            std::cerr << "  n: " << n;
            std::cerr << "  lcpMax: " << lcpMax;
            std::cerr << "  lcpAvrg: " << (TSize)(lcpAvrg + (lcpNumer + n/2) / n);
            std::cerr << "  sigma: " << sigma << std::endl;
        #endif
    }

    // HINT:
    // In contrast to the upper functions
    // createLCPTableInPlace expects the lcp table to be of size n
    template < typename TLCPTable,
               typename TText,
               typename TSA >
    void _createLCPTableRandomAccess(
        TLCPTable &LCP,
        TText const &s,
        TSA const &SA,
        Kasai const)
    {
        typedef typename Value<TSA>::Type TSize;

        #ifdef SEQAN_DEBUG_INDEX
            std::cerr << "--- CREATE LCP TABLE ---" << std::endl;
            std::cerr << "Start Kasai [random access,inplace]" << std::endl;
            if (sizeof(TSize) > 4)
                std::cerr << "WARNING: TSize size is greater 4 (Kasai)" << std::endl;
        #endif

        TSize n = length(s);
        if (n == 0) return;

        #ifdef SEQAN_DEBUG_INDEX
            TSize lcpMax = 0, lcpAvrg = 0, lcpNumer = 0, sigma = 1;    // for lcpMax, lcpMean, |Sigma|
        #endif

        TSize mark = ~(~0u>>1);
        TSize mask =   ~0u>>1;

        for(TSize i = 0; i < n; ++i)
            LCP[SA[i]] = i;

        SEQAN_PROMARK("Suffix-Array invertiert");
        #ifdef SEQAN_DEBUG_INDEX
            std::cerr << "Suffix-Array invertiert" << std::endl;
        #endif

        typename Iterator<TText const>::Type Ibegin = begin(s);
        typename Iterator<TText const>::Type I = Ibegin, J;
        for(TSize i = 0, h = 0, j, isa; i < n; ++i) {
            if ((isa = LCP[i] + 1) < n) {
                J = Ibegin + h + (j = SA[isa]);
                for(TSize hMax = _min(n - i, n - j); h < hMax && *I == *J; ++I, ++J, ++h) ;
                LCP[i] = h | mark;
                #ifdef SEQAN_DEBUG_INDEX
                    if ((lcpNumer += h) > n) {
                        lcpNumer -= n;
                        ++lcpAvrg;
                    }
                    if (lcpMax < h) lcpMax = h;
                    if (!h) ++sigma;
                #endif
            }
            if (h) --h;
            else ++I;
        }
        LCP[SA[n - 1]] = mark;
        SEQAN_PROMARK("permutierte LCP-Tabelle erzeugt");
        #ifdef SEQAN_DEBUG_INDEX
            std::cerr << "permutierte LCP-Tabelle erzeugt" << std::endl;
        #endif
        for(TSize i = 0, j, tmp; i < n; ++i)
            if (LCP[i] & mark) {
                j = i;
                tmp = LCP[j];
                while (SA[j] != i) {
                    LCP[j] = LCP[SA[j]] & mask;
                    j = SA[j];
                }
                LCP[j] = tmp & mask;
            }
        #ifdef SEQAN_DEBUG_INDEX
            std::cerr << "LCP-Tabelle erzeugt" << std::endl;
        #endif

        #ifdef SEQAN_DEBUG_INDEX
            std::cerr << "  n: " << n;
            std::cerr << "  lcpMax: " << lcpMax;
            std::cerr << "  lcpAvrg: " << (TSize)(lcpAvrg + (lcpNumer + n/2) / n);
            std::cerr << "  sigma: " << sigma << std::endl;
        #endif
    }


    // Kasai in-place for multiple sequences
    template < typename TLCPTable,
               typename TString,
               typename TSpec,
               typename TSA >
    void _createLCPTableRandomAccess(
        TLCPTable &LCP,
        StringSet<TString, TSpec> const &sset,
        TSA const &SA,
        Kasai const)
    {
        typedef StringSet<TString, TSpec>                            TStringSet;
        typedef typename Concatenator<TStringSet const>::Type        TText;
        typedef typename StringSetLimits<TStringSet const>::Type    TLimitsString;
//        typedef typename Value<TSA>::Type                            TPair;
        typedef Pair<
            typename Size<TStringSet>::Type,
            typename Size<TString>::Type>                            TPair;
        typedef PairDecrementer_<TPair, TLimitsString>                TDecrementer;
        typedef typename Value<TLCPTable>::Type                        TSize;

        #ifdef SEQAN_DEBUG_INDEX
            std::cerr << "--- CREATE LCP TABLE ---" << std::endl;
            std::cerr << "Start Kasai [random access,inplace,stringset]" << std::endl;
            if (sizeof(TSize) > 4)
                std::cerr << "WARNING: TSize size is greater 4 (Kasai)" << std::endl;
        #endif

        TText &s = concat(sset);
        TSize n = length(s);

        if (n == 0) return;

        #ifdef SEQAN_DEBUG_INDEX
            TSize lcpMax = 0, lcpAvrg = 0, lcpNumer = 0, sigma = 1;    // for lcpMax, lcpMean, |Sigma|
        #endif

        TSize mark = ~(~(TSize)0ul >> 1);
        TSize mask =   ~(TSize)0ul >> 1;

        TLimitsString const &limits = stringSetLimits(sset);
        {
            typename Iterator<TSA const>::Type itSA = begin(SA);
            for(TSize i = 0; i < n; ++i, ++itSA)
                LCP[posGlobalize(*itSA, limits)] = i;
        }

        SEQAN_PROMARK("Suffix-Array invertiert");
        #ifdef SEQAN_DEBUG_INDEX
            std::cerr << "Suffix-Array invertiert" << std::endl;
        #endif

        typename Iterator<TText const>::Type Ibegin = begin(s);
        typename Iterator<TText const>::Type I = Ibegin, J;

        TDecrementer dec(limits);

        for(TSize i = 0, h = 0, j, isa; i < n; ++i, --dec) {
            if ((isa = LCP[i] + 1) < n) {
                j = posGlobalize(SA[isa], limits);
                J = Ibegin + h + j;

                for(TSize hMax = _min(getValueI2((TPair)dec), n - j); h < hMax && *I == *J; ++I, ++J, ++h) ;
                LCP[i] = h | mark;
                #ifdef SEQAN_DEBUG_INDEX
                    if ((lcpNumer += h) > n) {
                        lcpNumer -= n;
                        ++lcpAvrg;
                    }
                    if (lcpMax < h) lcpMax = h;
                    if (!h) ++sigma;
                #endif
            }
            if (h)
                --h;
            else
                ++I;
        }

        LCP[posGlobalize(SA[n - 1], limits)] = mark;

        SEQAN_PROMARK("permutierte LCP-Tabelle erzeugt");
        #ifdef SEQAN_DEBUG_INDEX
            std::cerr << "permutierte LCP-Tabelle erzeugt" << std::endl;
        #endif
        for(TSize sa_j, i = 0, j, tmp; i < n; ++i)
            if (LCP[i] & mark) {
                j = i;
                tmp = LCP[j];
                sa_j = posGlobalize(SA[j], limits);
                while (sa_j != i) {
                    LCP[j] = LCP[sa_j] & mask;
                    j = sa_j;
                    sa_j = posGlobalize(SA[j], limits);
                }
                LCP[j] = tmp & mask;
            }
        #ifdef SEQAN_DEBUG_INDEX
            std::cerr << "LCP-Tabelle erzeugt" << std::endl;
        #endif

        #ifdef SEQAN_DEBUG_INDEX
            std::cerr << "  n: " << n;
            std::cerr << "  lcpMax: " << lcpMax;
            std::cerr << "  lcpAvrg: " << (TSize)(lcpAvrg + (lcpNumer + n/2) / n);
            std::cerr << "  sigma: " << sigma << std::endl;
        #endif
    }


//}

}

#endif
