// ==========================================================================
//                 SeqAn - The Library for Sequence Analysis
// ==========================================================================
// Copyright (c) 2006-2010, 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_BWT_H
#define SEQAN_HEADER_INDEX_BWT_H

namespace SEQAN_NAMESPACE_MAIN
{
	
//namespace SEQAN_NAMESPACE_PIPELINING
//{

	struct Bwt {};


    //////////////////////////////////////////////////////////////////////////////
    // external Bwt algorithm
    //////////////////////////////////////////////////////////////////////////////


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

	//////////////////////////////////////////////////////////////////////////////
    // bwt class
    template < typename TTextInput, typename TSuffixArrayInput >
    struct Pipe< Bundle2< TTextInput, TSuffixArrayInput >, Bwt >
    {
        // *** SPECIALIZATION ***

        typedef Pipe< TSuffixArrayInput, Counter > TSA;
		                                typedef typename Size<TTextInput>::Type	TSize;
		typedef Pool< TypeOf_(TSA), MapperSpec< MapperConfigSize< filterI1<TypeOf_(TSA)>, TSize> > > TInverter;
        typedef Pipe< TInverter, Filter< filterI2<TypeOf_(TInverter)> > > TCounterFilter;
		typedef Pipe< TTextInput, Shifter< -1, false > > TShiftText;

		typedef Pipe< Bundle2< TCounterFilter, TShiftText >, Joiner > TJoiner;
		typedef Pool< TypeOf_(TJoiner), MapperSpec< MapperConfigSize< filterI1<TypeOf_(TJoiner)>, TSize> > > TLinearMapper;
        typedef Pipe< TLinearMapper, Filter< filterI2<TypeOf_(TLinearMapper)> > > TFilter;

        TLinearMapper		mapper;
		TFilter				in;
        
        Pipe():
            in(mapper) {}

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

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

            // *** INSTANTIATION ***

			TSA							sa(suffixArrayIn);
			TInverter					inverter;
			TCounterFilter				filter(inverter);
			
            #ifdef SEQAN_DEBUG_INDEX
				::std::cerr << "  invert suffix array" << ::std::endl;
            #endif
			inverter << sa;
			SEQAN_PROMARK("Suffix-Array invertiert");

			TShiftText					shifter(textIn);
			TJoiner						joiner(bundle2(filter, shifter));
			
            #ifdef SEQAN_DEBUG_INDEX
                ::std::cerr << "  de-invert suffix array" << ::std::endl;
            #endif
			mapper << joiner;
			SEQAN_PROMARK("Suffix-Array linearisiert");

            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, Bwt > &me, Bundle2< TTextInput_, TSuffixArrayInput_ > const &bundleIn) {
 	    return me.process(bundleIn.in1, bundleIn.in2);
    }



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


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

	template <typename InType, typename TLimitsString, typename Result = typename Value<TLimitsString>::Type>
	struct _filterGlobalizer : public ::std::unary_function<InType,Result> {
		TLimitsString const &limits;
		_filterGlobalizer(TLimitsString const &_limits) : limits(_limits) {}
        inline Result operator()(const InType& x) const
        {
			return posGlobalize(x, limits);
		}
    };


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

										typedef _filterGlobalizer<TypeOf_(TSuffixArrayInput), TLimitsString, TSizeOf_(TSuffixArrayInput)> filter_globalizer_t;
		typedef Pipe< TSuffixArrayInput, Filter<filter_globalizer_t> > TGlobalizer;
        typedef Pipe< TGlobalizer, Counter > TSA;
		                                typedef typename Size<TTextInput>::Type	TSize;
		typedef Pool< TypeOf_(TSA), MapperSpec< MapperConfigSize< filterI1<TypeOf_(TSA)>, TSize> > > TInverter;
        typedef Pipe< TInverter, Filter< filterI2<TypeOf_(TInverter)> > > TCounterFilter;
		typedef Pipe< TTextInput, Shifter< -1, false > > TShiftText;

		typedef Pipe< Bundle2< TCounterFilter, TShiftText >, Joiner > TJoiner;
		typedef Pool< TypeOf_(TJoiner), MapperSpec< MapperConfigSize< filterI1<TypeOf_(TJoiner)>, TSize> > > TLinearMapper;
        typedef Pipe< TLinearMapper, Filter< filterI2<TypeOf_(TLinearMapper)> > > TFilter;

		TTextInput			*textIn;
		TSuffixArrayInput	*suffixArrayIn;
        TLinearMapper		mapper;
		TFilter				in;

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

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

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

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

            // *** INSTANTIATION ***

			for(int i=0;i<length(limits);++i)
				::std::cout << limits[i]<<"  ";
			::std::cout<<::std::endl;
			
			TGlobalizer					globalizer(suffixArrayIn, limits);
			TSA							sa(globalizer);
			TInverter					inverter;
			TCounterFilter				filter(inverter);
			
            #ifdef SEQAN_DEBUG_INDEX
                ::std::cerr << "  invert suffix array" << ::std::endl;
            #endif
			inverter << sa;
			SEQAN_PROMARK("Suffix-Array invertiert");

			TShiftText					shifter(textIn);
			TJoiner						joiner(bundle2(filter, shifter));
			
            #ifdef SEQAN_DEBUG_INDEX
                ::std::cerr << "  de-invert suffix array" << ::std::endl;
            #endif
			mapper << joiner;
			SEQAN_PROMARK("Suffix-Array linearisiert");

            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 "bwt << pipe" or "bwt_t bwt(pipe); bwt.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<Bwt, TPair, TLimitsString> > &me, Bundle2< TTextInput_, TSuffixArrayInput_ > const &bundleIn) {
 	    return me.process(bundleIn.in1, bundleIn.in2);
    }



    //////////////////////////////////////////////////////////////////////////////
    // internal Bwt algorithm
    //////////////////////////////////////////////////////////////////////////////


    template < typename TBWT,
               typename TText,
               typename TSA >
    void createBWTableInt(
		TBWT &bwt,
		TText const &s,
		TSA const &SA)
	{
		typedef typename Value<TBWT>::Type		TValue;
		typedef typename GetValue<TSA>::Type	TSAValue;
		typedef typename Size<TSA>::Type		TSize;

		TSize n = length(s);

		for (TSize i = 0; i < n; ++i)
		{
			TSAValue sa = getValue(SA, i);
			if (sa != 0)
				bwt[i] = getValue(s, sa - 1);
			else
				bwt[i] = TValue();
//				bwt[i] = getValue(s, n - 1);
		}
	}

    template < typename TBWT,
               typename TString,
			   typename TSpec,
               typename TSA >
    void createBWTableInt(
		TBWT &bwt,
		StringSet<TString, TSpec> const &s,
		TSA const &SA)
	{
		typedef typename Value<TBWT>::Type		TValue;
		typedef typename GetValue<TSA>::Type	TSAValue;
		typedef typename Size<TSA>::Type		TSize;

		TSize n = lengthSum(s);
		Pair<unsigned, typename Size<TString>::Type> loc;

		for (TSize i = 0; i < n; ++i)
		{
			posLocalize(loc, getValue(SA, i), stringSetLimits(s));
			if (loc.i2 != 0)
				bwt[i] = s[loc.i1][loc.i2 - 1];
			else
				if (loc.i1 != 0)
					bwt[i] = s[loc.i1 - 1][length(s[loc.i1 - 1]) - 1];
				else
					bwt[i] = TValue();
//					bwt[i] = getValue(s, n - 1);
		}
	}

//}

}

#endif