// ==========================================================================
//                 SeqAn - The Library for Sequence Analysis
// ==========================================================================
// Copyright (c) 2006-2016, 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_PIPE_BASE_H
#define SEQAN_HEADER_PIPE_BASE_H

namespace seqan {

    // shortcuts to ease pipeline construction
    #define TypeOf_(TObject)  typename Value<TObject>::Type
    #define TSizeOf_(TObject) typename Size<TObject>::Type

/*!
 * @class Pipe
 * @headerfile <seqan/pipe.h>
 * @brief Pipes are pop-passive pipeline modules.
 *
 * @signature template <typename TInput, typename TSpec>
 *            class Pipe;
 *
 * @tparam TSpec  The specializing type.
 * @tparam TInput The type of the pipeline module this module reads from.  Use Bundle2, Bundle3, etc. to read
 *                from more than one module.
 *
 * Use @link Pipe#Value @endlink to get the output type of a given Pipe (returns <tt>Value&lt;TInput&gt;::Type</tt> by
 * default).
 *
 * Use Size to get the size type of a given Pipe (returns <tt>Size&lt;TInput&gt;::Type</tt> by default).
 */

/*!
 * @fn Pipe::Pipe
 * @brief Constructor
 *
 * @signature Pipe::Pipe(in);
 *
 * @param[in] in Reference to an input pipe.
 */

    template < typename TInput, typename TSpec >
    struct Pipe {
        TInput &in;
        Pipe(TInput &_in): in(_in) {}
    };

    // base class for multiple sequence algorithms
    // to hold extra information about desired position type (TPair)
    // and the type storing absolute sequence offsets (TLimitsString)
    template <typename TSpec, typename TPair, typename TLimitsString>
    struct Multi;

/*!
 * @class Bundle2
 * @headerfile <seqan/pipe.h>
 * @brief Stores references to two arbitrary objects.
 *
 * @signature template <typename TInput1, typename TInput2>
 *            class Bundle2;
 *
 * @tparam TInput1 The type of the first object.
 * @tparam TInput2 The type of the second object.
 *
 * Primarily used as an adaptor for pipes with two sources.
 *
 * @see bundle2
 *
 * @var TInput1 Bundle2::in1;
 * @brief TInput1 reference
 *
 * @var TInput2 Bundle2::in2;
 * @brief TInput2 reference
 */

    // pipe input adapter 2->1 pipe
    template < typename TInput1, typename TInput2 >
    struct Bundle2 {
        typedef TInput1 Input1;
        typedef TInput2 Input2;
        TInput1 &in1;
        TInput2 &in2;
        Bundle2(TInput1 &_in1, TInput2 &_in2): in1(_in1),in2(_in2) {}
    };

/*!
 * @fn bundle2
 * @headerfile <seqan/pipe.h>
 * @brief Returns a bundle of two objects.
 *
 * @signature TBundle bundle2(in1, in2);
 *
 * @param[in] in1 First object.
 * @param[in] in2 Second object.
 *
 * @return TBundle A Bundle2 with references to <tt>in1</tt> and <tt>in2</tt>.
 *
 * @see Bundle2
 */

    template < typename TInput1, typename TInput2 >
    inline Bundle2< TInput1, TInput2 >
    bundle2(TInput1 &_in1, TInput2 &_in2) {
        return Bundle2< TInput1, TInput2 >(_in1, _in2);
    }
/*!
 * @class Bundle3
 *
 * @brief Stores references to three arbitrary objects.
 *
 * @signature template <typename TInput1, typename TInput2, typename TInput3>
 *            struct Bundle3;
 *
 * @tparam TInput3 The type of the third object.
 * @tparam TInput2 The type of the second object.
 * @tparam TInput1 The type of the first object.
 *
 * Primarily used as an adaptor for pipes with three sources.
 *
 * @see bundle3
 *
 * @var TInput1 Bundle3::in1;
 * @brief TInput1 reference
 *
 * @var TInput2 Bundle3::in2;
 * @brief TInput2 reference
 *
 * @var TInput3 Bundle3::in3;
 * @brief TInput3 reference
 */

    // pipe input adapter 3->1 pipe
    template < typename TInput1, typename TInput2, typename TInput3 >
    struct Bundle3 {
        typedef TInput1 Input1;
        typedef TInput2 Input2;
        typedef TInput3 Input3;
        TInput1 &in1;
        TInput2 &in2;
        TInput3 &in3;
        Bundle3(TInput1 &_in1, TInput2 &_in2, TInput3 &_in3): in1(_in1),in2(_in2),in3(_in3) {}
    };

/*!
 * @fn bundle3
 * @headerfile <seqan/pipe.h>
 * @brief Returns a bundle of three objects.
 *
 * @signature TBundle bundle3(in1, in2, in3);
 *
 * @param[in] in1 First object.
 * @param[in] in2 Second object.
 * @param[in] in3 Third object.
 *
 * @return TBundle A Bundle3 with references to <tt>in1</tt>, <tt>in2</tt>, and <tt>in3</tt>.
 *
 * @see Bundle3
 */

    template < typename TInput1, typename TInput2, typename TInput3 >
    inline Bundle3< TInput1, TInput2, TInput3 >
    bundle3(TInput1 &_in1, TInput2 &_in2, TInput3 &_in3) {
        return Bundle3< TInput1, TInput2, TInput3 >(_in1, _in2, _in3);
    }

/*!
 * @class Bundle5
 * @headerfile <seqan/pipe.h>
 * @brief Stores references to five arbitrary objects.
 *
 * @signature template <typename TInput1, typename TInput2, typename TInput3, typename TInput4, typename TInput5>
 *            class Bundle5;
 *
 * @tparam TInput1 The type of the first object.
 * @tparam TInput2 The type of the second object.
 * @tparam TInput3 The type of the third object.
 * @tparam TInput4 The type of the fourth object.
 * @tparam TInput5 The type of the fifth object.
 *
 * Primarily used as an adaptor for pipes with five sources.
 *
 * @see bundle5
 *
 * @var TInput1 Bundle5::in1;
 * @brief TInput1 reference
 *
 * @var TInput2 Bundle5::in2;
 * @brief TInput2 reference
 *
 * @var TInput3 Bundle5::in3;
 * @brief TInput3 reference
 *
 * @var TInput4 Bundle5::in4;
 * @brief TInput4 reference
 *
 * @var TInput5 Bundle5::in5;
 * @brief TInput5 reference
 */

    // pipe input adapter 5->1 pipe
    template < typename TIn1, typename TIn2, typename TIn3, typename TIn4, typename TIn5 >
    struct Bundle5 {
        TIn1 &in1; TIn2 &in2;
        TIn3 &in3; TIn4 &in4;
        TIn5 &in5;
        Bundle5(TIn1& _in1, TIn2& _in2,
                TIn3& _in3, TIn4& _in4,
                TIn5& _in5):    in1(_in1),in2(_in2),
                                in3(_in3),in4(_in4),
                                in5(_in5) {}
    };

/*!
 * @fn bundle5
 * @headerfile <seqan/pipe.h>
 * @brief Returns a bundle of five objects.
 *
 * @signature TBundle bundle5(in1, in2, in3, in4, in5);
 *
 * @param[in] in1 First object.
 * @param[in] in2 Second object.
 * @param[in] in3 Third object.
 * @param[in] in4 Fourth object.
 * @param[in] in5 Fifth object.
 *
 * @return TBundle A Bundle5 with references to <tt>in1</tt>, <tt>in2</tt>, <tt>in3</tt>, <tt>in4</tt>,
 *                 and <tt>in5</tt>.
 *
 * @see Bundle5
 */

    template < typename TIn1, typename TIn2, typename TIn3, typename TIn4, typename TIn5 >
    inline Bundle5< TIn1, TIn2, TIn3, TIn4, TIn5 >
    bundle5(TIn1 &_in1, TIn2 &_in2, TIn3 &_in3, TIn4 &_in4, TIn5 &_in5) {
        return Bundle5< TIn1, TIn2, TIn3, TIn4, TIn5 >(_in1, _in2, _in3, _in4, _in5);
    }

    template < typename TValue, typename TSize >
    struct AbstractSource {};

/*!
 * @mfn Pipe#Value
 * @brief Return value type of the Pipe specialization.
 *
 * @signature Value<TPipe>::Type;
 *
 * @tparam TPipe The Pipe specialization to query.
 *
 * @return Type The resulting value type.
 */

    template < typename TValue, typename TSize >
    struct Value< Pipe<void, AbstractSource<TValue, TSize> > > {
        typedef TValue Type;
    };

/*!
 * @mfn Pipe#Size
 * @brief Return size type of the Pipe specialization.
 *
 * @signature Size<TPipe>::Type;
 *
 * @tparam TPipe The Pipe specialization to query.
 *
 * @return Type The resulting size type.
 */

    template < typename TValue, typename TSize >
    struct Size< Pipe<void, AbstractSource<TValue, TSize> > > {
        typedef TSize Type;
    };

    template < typename TInput, typename TSpec >
    struct Value< Pipe<TInput, TSpec> > {
        typedef typename Value<TInput>::Type Type;
    };

    template < typename TInput, typename TSpec >
    struct Size< Pipe<TInput, TSpec> > {
        typedef typename Size<TInput>::Type Type;
    };

    template < typename TInput1, typename TInput2 >
    struct Size< Bundle2< TInput1, TInput2 > > {
        typedef typename Size<TInput1>::Type Type;
    };

    template < typename TInput1, typename TInput2, typename TInput3 >
    struct Size< Bundle3< TInput1, TInput2, TInput3 > > {
        typedef typename Size<TInput1>::Type Type;
    };

    template < typename TIn1, typename TIn2, typename TIn3, typename TIn4, typename TIn5 >
    struct Size< Bundle5< TIn1, TIn2, TIn3, TIn4, TIn5 > > {
        typedef typename Size<TIn1>::Type Type;
    };

    template < typename TInput, typename TSpec >
    struct Position< Pipe<TInput, TSpec> > {
        typedef typename Size<Pipe<TInput, TSpec> >::Type Type;
    };

    template < typename TInput, typename TSpec >
    struct Difference< Pipe<TInput, TSpec> > {
        typedef typename MakeSigned_<typename Size<Pipe<TInput, TSpec> >::Type>::Type Type;
    };
/*
    template < typename TInput, typename TSpec >
    struct Iterator< Pipe<TInput, TSpec> >;

    template < typename TInput, typename TSpec >
    struct Iterator< Pipe<TInput, TSpec> const >:
        Iterator< Pipe<TInput, TSpec> > {};
*/

    template <typename T>
    struct Source;

    template <typename TInput, typename TSpec>
    struct Source<Pipe<TInput, TSpec> >
    {
        typedef TInput Type;
    };

    template < typename TInput, typename TSpec >
    inline TInput const &
    source(Pipe<TInput, TSpec> const &me) {
        return me.in;
    }

    template < typename TInput, typename TSpec >
    inline TInput &
    source(Pipe<TInput, TSpec> &me) {
        return me.in;
    }

/*!
 * @fn Pipe#length
 * @headerfile <seqan/pipe.h>
 * @brief Length of the pipe.
 *
 * @signature TSize length(pipe);
 *
 * @param[in] pipe  The Pipe to query for its size.
 *
 * @return    TSize The size of the pipe.
 */

    template < typename TInput, typename TSpec >
    inline typename Size< Pipe<TInput, TSpec> >::Type
    length(Pipe<TInput, TSpec> const &me) {
        return length(me.in);
    }

    template < typename TInput1, typename TInput2 >
    inline typename Size< Bundle2<TInput1, TInput2> >::Type
    length(Bundle2<TInput1, TInput2> const &me) {
        return length(me.in1);
    }

    template < typename TInput1, typename TInput2, typename TInput3 >
    inline typename Size< Bundle3<TInput1, TInput2, TInput3> >::Type
    length(Bundle3<TInput1, TInput2, TInput3> const &me) {
        return length(me.in1);
    }

    template < typename TIn1, typename TIn2, typename TIn3, typename TIn4, typename TIn5 >
    inline typename Size< Bundle5<TIn1, TIn2, TIn3, TIn4, TIn5> >::Type
    length(Bundle5<TIn1, TIn2, TIn3, TIn4, TIn5> const &me) {
        return length(me.in1);
    }

//////////////////////////////////////////////////////////////////////////////


    template < typename TInput, typename TSpec >
    inline typename Size< Pipe<TInput, TSpec> >::Type
    countSequences(Pipe<TInput, TSpec> const &me) {
        return countSequences(me.in);
    }

    template < typename TInput1, typename TInput2 >
    inline typename Size< Bundle2<TInput1, TInput2> >::Type
    countSequences(Bundle2<TInput1, TInput2> const &me) {
        return countSequences(me.in1);
    }

    template < typename TInput1, typename TInput2, typename TInput3 >
    inline typename Size< Bundle3<TInput1, TInput2, TInput3> >::Type
    countSequences(Bundle3<TInput1, TInput2, TInput3> const &me) {
        return countSequences(me.in1);
    }

    template < typename TIn1, typename TIn2, typename TIn3, typename TIn4, typename TIn5 >
    inline typename Size< Bundle5<TIn1, TIn2, TIn3, TIn4, TIn5> >::Type
    countSequences(Bundle5<TIn1, TIn2, TIn3, TIn4, TIn5> const &me) {
        return countSequences(me.in1);
    }

/*!
 * @fn Pipe#front
 * @headerfile <seqan/pipe.h>
 * @brief Gets the first element of the remaining stream.
 *
 * @signature TValue front(object);
 *
 * @param[in] object A pop-passive pipeline module.
 *
 * @return TValue The first element of the remaining input stream.  Return type is <tt>Value&lt;TObject&gt;::Type</tt>
 *                for <tt>object</tt> type <tt>TObject</tt>.
 *
 * Pipe#front or Pipe#pop can only be called within a read process surrounded by beginRead and endRead.
 *
 * @see Pipe#pop
 */

    template < typename TInput, typename TSpec, typename TValue >
    inline typename Value< Pipe<TInput, TSpec> >::Type const &
    front(Pipe<TInput, TSpec> &me) {
        return *me;
    }

/*!
 * @fn Pipe#pop
 * @headerfile <seqan/pipe.h>
 * @brief Pops the first element of the remaining stream.
 *
 * @signature void pop(pipe[, ref]);
 *
 * @param[in,out] pipe A pop-passive pipeline module.
 * @param[out]    ref    Reference to the result.  Result type is <tt>Value&lt;TObject&gt;::Type</tt> for <tt>object</tt>
 *                       type <tt>TObject</tt>.  Returns the first element of the remaining input stream.
 *
 * In contrast to Pipe#front this function also steps one element further.
 *
 * Pipe#front or Pipe#pop can only be called within a read process surrounded by beginRead and endRead.
 */

    template < typename TInput, typename TSpec, typename TValue >
    inline void pop(Pipe<TInput, TSpec> &me, TValue &Ref_) {
        Ref_ = *me;
        ++me;
    }

    template < typename TInput, typename TSpec >
    inline void pop(Pipe<TInput, TSpec> &me) {
        ++me;
    }

/*!
 * @fn Pipe#atEnd
 * @brief Check whether the @link Pipe @endlink object is at end.
 *
 * @signature bool atEnd(pipe);
 *
 * @param[in] pipe The @link Pipe @endlink object to query.
 *
 * @return bool true in case of the pipe being at the end, false otherwise.
 */

    //////////////////////////////////////////////////////////////////////////////
    // pipe flow control

    struct ControlEof_;            // end of stream
    struct ControlEos_;            // end of sequence (for multiple sequences)
    struct ControlClear_;        // clear previous pool
    struct ControlBeginRead_;    // begin read process
    struct ControlEndRead_;        // end read process

    typedef Tag<ControlEof_>        ControlEof;
    typedef Tag<ControlEos_>        ControlEos;
    typedef Tag<ControlClear_>        ControlClear;
    typedef Tag<ControlBeginRead_>    ControlBeginRead;
    typedef Tag<ControlEndRead_>    ControlEndRead;

    template < typename TInput, typename TSpec, typename TCommand >
    inline bool control(Pipe<TInput, TSpec> &me, TCommand const &command) {
        return control(me.in, command);
    }

    template < typename TInput, typename TSpec >
    inline bool eof(Pipe<TInput, TSpec> &me) {
        return control(me, ControlEof());
    }

    template < typename TInput, typename TSpec >
    inline bool eos(Pipe<TInput, TSpec> &me) {
        return control(me, ControlEos());
    }

    template < typename TInput, typename TSpec >
    inline bool clear(Pipe<TInput, TSpec> &me) {
        return control(me, ControlClear());
    }

/*!
 * @fn Pipe#beginRead
 * @headerfile <seqan/pipe.h>
 * @brief Initiates a read process.
 *
 * @signature bool beginRead(object);
 *
 * @param[in,out] object A pop-passive pipeline module.
 *
 * @return bool true on success, false on failure.
 *
 * <tt>beginRead</tt> rewinds the output stream, prepares <tt>object</tt> for succeeding reads, and typically calls
 * <tt>beginRead</tt> of the input pipeline modules.
 *
 * A read process must be terminated with endRead. Nested read processes are not allowed.
 *
 * @see Pipe#endRead
 */

    template < typename TInput, typename TSpec >
    inline bool beginRead(Pipe<TInput, TSpec> &me)
    {
        return control(me, ControlBeginRead());
    }

/*!
 * @fn Pipe#endRead
 * @headerfile <seqan/pipe.h>
 * @brief Terminates a read process.
 *
 * @signature bool endRead(object);
 *
 * @param[in,out] object A pop-passive pipeline module.
 *
 * @return bool true on success, false on failure.
 *
 * <tt>endRead</tt> closes the output stream, frees resources possibly allocated by beginRead, and typically calls
 * <tt>endRead</tt> of the input pipeline modules.
 *
 * @see Pipe#beginRead
 */

    template < typename TInput, typename TSpec >
    inline bool endRead(Pipe<TInput, TSpec> &me) {
        return control(me, ControlEndRead());
    }


    //////////////////////////////////////////////////////////////////////////////
    // 2->1 pipe flow control
    template < typename TInput1, typename TInput2, typename TCommand >
    inline bool control(Bundle2<TInput1, TInput2> &me, TCommand const &command) {
        return    control(me.in1, command) &&
                control(me.in2, command);
    }

    //////////////////////////////////////////////////////////////////////////////
    // 3->1 pipe flow control
    template < typename TInput1, typename TInput2, typename TInput3, typename TCommand >
    inline bool control(Bundle3<TInput1, TInput2, TInput3> &me, TCommand const &command) {
        return    control(me.in1, command) &&
                control(me.in2, command) &&
                control(me.in3, command);
    }

    //////////////////////////////////////////////////////////////////////////////
    // 5->1 pipe flow control
    template < typename TIn1, typename TIn2, typename TIn3, typename TIn4, typename TIn5, typename TCommand >
    inline bool control(Bundle5<TIn1, TIn2, TIn3, TIn4, TIn5 > &me, TCommand const &command) {
        return    control(me.in1, command) &&
                control(me.in2, command) &&
                control(me.in3, command) &&
                control(me.in4, command) &&
                control(me.in5, command);
    }
/*!
 * @fn Pipe#assign
 * @headerfile <seqan/pipe.h>
 * @brief Assigns one object to another object.
 *
 * @signature void assign(target, source);
 *
 * @param[out] target Reference to assign to.
 * @param[in]  source Value to assign.
 *
 * Assign value of source to target.
 */
    //////////////////////////////////////////////////////////////////////////////
    // pipe -> string

    // We cannot use the most-generic TObject as first argument, as operator << specialized somewhere else in
    // the first argument and here we need to specialize it in the second.
    template < typename TValue,
               typename TStringSpec,
               typename TInput,
               typename TSpec >
    inline void assign(String<TValue, TStringSpec> &dest, Pipe<TInput, TSpec> &src)
    {
        typedef typename Iterator<String<TValue, TStringSpec>, Standard >::Type TDestIter;
        resize(dest, length(src));
        beginRead(src);
        for (TDestIter _cur = begin(dest, Standard()), _end = end(dest, Standard()); _cur != _end; ++_cur, ++src)
            *_cur = *src;
        endRead(src);
    }

    template < typename TValue,
               typename TSegmentSpec,
               typename TInput,
               typename TSpec >
    inline void assign(Segment<TValue, TSegmentSpec> &dest, Pipe<TInput, TSpec> &src)
    {
        typedef typename Iterator<Segment<TValue, TSegmentSpec>, Standard >::Type TDestIter;
        resize(dest, length(src));
        beginRead(src);
        for (TDestIter _cur = begin(dest, Standard()), _end = end(dest, Standard()); _cur != _end; ++_cur, ++src)
            *_cur = *src;
        endRead(src);
    }

    template < typename TValue,
               typename TStringSpec,
               typename TInput,
               typename TSpec >
    inline void operator << (String<TValue, TStringSpec> &dest, Pipe<TInput, TSpec> &src)
    {
        assign(dest, src);
    }

    template < typename TValue,
               typename TSegmentSpec,
               typename TInput,
               typename TSpec >
    inline void operator << (Segment<TValue, TSegmentSpec> &dest, Pipe<TInput, TSpec> &src)
    {
        assign(dest, src);
    }

    //////////////////////////////////////////////////////////////////////////////
    // pipe -> out_stream
    template <typename TInput, typename TSpec>
    std::ostream& operator << (std::ostream &out, Pipe<TInput, TSpec> &src)
    {
        beginRead(src);
        while (!eof(src)) {
            out << *src << std::endl;
            ++src;
        }
        endRead(src);
        return out;
    }


    template < typename TObject, typename TSpec >
    struct BufferHandler;

    template <typename TObject, typename TSpec>
    struct Value<BufferHandler<TObject, TSpec> >
    {
        typedef Buffer<typename Value<TObject>::Type> Type;
    };



    template <typename TObject, typename TSpec>
    struct Handler;

    template <typename TObject, typename TSpec>
    struct Value<Handler<TObject, TSpec> >:
        public Value<TObject> {};

    // buffer-based read/write handler metafunctions
    template < typename TInput >
    struct BufReadHandler;

    template < typename TOutput >
    struct BufWriteHandler;



    //////////////////////////////////////////////////////////////////////////////
    // generic adapter for buffered readers/writers

    template <typename TValue, typename TSpec, typename TSize >
    inline void resize(Buffer<TValue, TSpec> &me, TSize size);

    struct AdapterSpec;

    template <typename TBufferHandler>
    struct Handler<TBufferHandler, AdapterSpec>
    {
        typedef typename Value<TBufferHandler>::Type        TBuffer;
        typedef typename Value<TBuffer>::Type               TValue;
        typedef typename Iterator<TBuffer, Standard>::Type  TIterator;

        TBufferHandler  handler;
        TBuffer            buffer;
        TIterator       cur;

        template < typename TObject >
        Handler(TObject &_object) :
            handler(_object), cur() {}

        inline bool begin()
        {
            buffer = handler.first();
            cur = seqan::begin(buffer, Standard());
            return true;
        }

        inline TValue const & front() const
        {
            return *cur;
        }

        inline void pop()
        {
            if (++cur == seqan::end(buffer, Standard()))
            {
                buffer = handler.next();
                cur = seqan::begin(buffer, Standard());
            }
        }

        inline void pop(TValue &Ref_)
        {
            Ref_ = *cur;
            pop();
        }

        inline void push(TValue const & Val_)
        {
            if (cur == seqan::end(buffer, Standard()))
            {
                buffer = handler.next();
                cur = seqan::begin(buffer, Standard());
            }
            *cur = Val_;
            ++cur;
        }

        inline bool eof() const
        {
            return length(buffer) == 0;
        }

        inline void end()
        {
            handler.end();
            resize(buffer, 0);
        }

        inline void process()
        {
            handler.process();
        }
    };

    template <typename TBufferHandler>
    struct Value<Handler<TBufferHandler, AdapterSpec> >:
        public Value<typename Value<TBufferHandler>::Type> {};

    // character-based read/write handler metafunctions
    template < typename TInput >
    struct ReadHandler
    {
        typedef Handler< typename BufReadHandler<TInput> ::Type, AdapterSpec > Type;
    };

    template < typename TOutput >
    struct WriteHandler
    {
        typedef Handler< typename BufWriteHandler<TOutput> ::Type, AdapterSpec > Type;
    };


    //////////////////////////////////////////////////////////////////////////////
    // pair incrementer
    //
    // used by pipes processing multiples sequences
    // for generating pairs (seqNo, seqOffs)

    template <typename TPair, typename TLimits>
    struct PairIncrementer_
    {
        typedef typename Iterator<TLimits const, Standard>::Type            TIter;
        typedef typename RemoveConst_<typename Value<TLimits>::Type>::Type  TSize;
        typedef typename Value<TPair, 2>::Type                              TOffset;

        TIter   it, itEnd;
        TSize   old;
        TOffset localEnd;

        TPair pos;
        inline operator TPair () const
        {
            return pos;
        }

        inline TPair const & operator++ ()
        {
            TOffset i2 = getValueI2(pos) + 1;
            if (i2 >= localEnd)
            {
                i2 = 0;
                localEnd = 0;
                while (!localEnd && (it != itEnd))
                {
                    typename Value<TPair,1>::Type i1 = getValueI1(pos);
                    assignValueI1(pos, i1 + 1);
                    localEnd = (*it - old);
                    // test for overflows
                    SEQAN_ASSERT_LT_MSG(i1, getValueI1(pos), "Overflow detected. Use a bigger type for the *first* value in the SAValue pair!");
                    SEQAN_ASSERT_EQ_MSG((TSize)localEnd, (*it - old), "Overflow detected. Use a bigger type for the *second* value in the SAValue pair!");
                    old = *it;
                    ++it;
                }
                if (!localEnd && it == itEnd)
                    assignValueI1(pos, getValueI1(pos) + 1);    // set pos behind the last sequence
            }
            assignValueI2(pos, i2);
            return pos;
        }
    };

    template <typename TPair, typename TLimits, typename TLimits2>
    void setHost(PairIncrementer_<TPair, TLimits> &me, TLimits2 const &limits)
    {
        me.it = begin(limits, Standard());
        me.itEnd = end(limits, Standard());
        me.old = 0;
        me.localEnd = 0;
        me.pos = TPair(0, 0);
        if (length(limits) > 1)
        {
            ++me.it;
            ++me;
            assignValueI1(me.pos, getValueI1(me.pos) - 1);
        }
    }

    template <typename TPair, typename TLimits, typename TLimits2>
    void setHost(PairIncrementer_<TPair, TLimits> &me, TLimits2 &limits)
    {
        setHost(me, const_cast<TLimits2 const &>(limits));
    }
//____________________________________________________________________________

    template <typename TPair, typename TLimits>
    TPair const & value(PairIncrementer_<TPair, TLimits> const &me) {
        return me.pos;
    }

    template <typename TPair, typename TLimits>
    TPair & value(PairIncrementer_<TPair, TLimits> &me) {
        return me.pos;
    }


    //////////////////////////////////////////////////////////////////////////////
    // pair decrementer
    //
    // used by pipes processing multiples sequences
    // for generating pairs (seqNo, seqOffs)

    template <typename TPair, typename TLimits, unsigned m = 0>
    struct PairDecrementer_
    {
        typedef typename Iterator<TLimits const, Standard>::Type            TIter;
        typedef typename RemoveConst_<typename Value<TLimits>::Type>::Type  TSize;

        TIter       it, itEnd;
        TSize       old;
        TPair        pos;
        unsigned    residue;

        PairDecrementer_() : it(), itEnd(), old(), pos(), residue() {}
        PairDecrementer_(TLimits const &_limits) : it(), itEnd(), old(), pos(), residue()
        { setHost(*this, _limits); }

        inline operator TPair () const
        {
            return pos;
        }

        inline TPair const & operator-- ()
        {
            typename Value<TPair,2>::Type i2 = getValueI2(pos);
            if (i2 > 1)
            {
                --i2;
                if (residue == 0) residue = m;
                --residue;
            }
            else
            {
                i2 = 0;
                while (!i2 && (it != itEnd))
                {
                    typename Value<TPair,1>::Type i1 = getValueI1(pos);
                    assignValueI1(pos, i1 + 1);
                    i2 = (*it - old);
                    // test for overflows
                    SEQAN_ASSERT_LT_MSG(i1, getValueI1(pos), "Overflow detected. Use a bigger type for the *first* value in the SAValue pair!");
                    SEQAN_ASSERT_EQ_MSG((TSize)i2, *it - old, "Overflow detected. Use a bigger type for the *second* value in the SAValue pair!");
                    old = *it;
                    ++it;
                }
                residue = i2 % m;
            }
            assignValueI2(pos, i2);
            return pos;
        }
    };

    template <typename TPair, typename TLimits, unsigned m, typename TLimits2>
    void setHost(PairDecrementer_<TPair, TLimits, m> &me, TLimits2 const &limits)
    {
        me.it = begin(limits);
        me.itEnd = end(limits);
        me.old = 0;
        me.pos = TPair(0, 0);
        if (length(limits) > 1)
        {
            ++me.it;
            --me;
            assignValueI1(me.pos, getValueI1(me.pos) - 1);
        } else
            me.residue = 0;
    }

    template <typename TPair, typename TLimits, unsigned m, typename TLimits2>
    void setHost(PairDecrementer_<TPair, TLimits, m> &me, TLimits2 &limits)
    {
        setHost(me, const_cast<TLimits const &>(limits));
    }
//____________________________________________________________________________

    template <typename TPair, typename TLimits>
    struct PairDecrementer_<TPair, TLimits, 0>
    {
        typedef typename Iterator<TLimits const, Standard>::Type            TIter;
        typedef typename RemoveConst_<typename Value<TLimits>::Type>::Type  TSize;

        TIter       it, itEnd;
        TSize       old;
        TPair        pos;

        PairDecrementer_() {}
        PairDecrementer_(TLimits const &_limits) { setHost(*this, _limits); }

        inline operator TPair () const {
            return pos;
        }

        inline TPair const & operator-- ()
        {
            typename Value<TPair,2>::Type i2 = getValueI2(pos);
            if (i2 > 1)
                --i2;
            else
            {
                i2 = 0;
                while (!i2 && (it != itEnd))
                {
                    typename Value<TPair,1>::Type i1 = getValueI1(pos);
                    assignValueI1(pos, i1 + 1);
                    i2 = (*it - old);
                    // test for overflows
                    SEQAN_ASSERT_LT_MSG(i1, getValueI1(pos), "Overflow detected. Use a bigger type for the *first* value in the SAValue pair!");
                    SEQAN_ASSERT_EQ_MSG((TSize)i2, *it - old, "Overflow detected. Use a bigger type for the *second* value in the SAValue pair!");
                    old = *it;
                    ++it;
                }
            }
            assignValueI2(pos, i2);
            return pos;
        }
    };

    template <typename TPair, typename TLimits, typename TLimits2>
    void setHost(PairDecrementer_<TPair, TLimits, 0> &me, TLimits2 const &limits) {
        me.it = begin(limits);
        me.itEnd = end(limits);
        me.old = 0;
        assignValueI1(me.pos, 0);
        assignValueI2(me.pos, 0);
        if (length(limits) > 1) {
            ++me.it;
            --me;
            assignValueI1(me.pos, getValueI1(me.pos) - 1);
        }
    }

    template <typename TPair, typename TLimits, typename TLimits2>
    void setHost(PairDecrementer_<TPair, TLimits, 0> &me, TLimits2 &limits)
    {
        setHost(me, const_cast<TLimits const &>(limits));
    }
//____________________________________________________________________________

    template <typename TPair, typename TLimits, unsigned m>
    TPair const & value(PairDecrementer_<TPair, TLimits, m> const &me) {
        return me.pos;
    }

    template <typename TPair, typename TLimits, unsigned m>
    TPair & value(PairDecrementer_<TPair, TLimits, m> &me) {
        return me.pos;
    }

}

#endif
