// ==========================================================================
//                 SeqAn - The Library for Sequence Analysis
// ==========================================================================
// Copyright (c) 2006-2024, 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_SOURCE_H
#define SEQAN_HEADER_PIPE_SOURCE_H

namespace seqan2
{

/*
    template < typename TValue >
    struct Size< Pipe< TValue*, Source<> > > {
        typedef ptrdiff_t Type;
    };
*/

/*!
 * @class Source
 * @extends Pipe
 * @headerfile <seqan/pipe.h>
 * @brief Pipelining adaptor for arbitrary containers or iterators.
 *
 * @signature template <typename TInput>
 *            class Pipe<TInput, Source<> >;
 *
 * @tparam TInput The type of container or iterator this module reads from.
 */


    //////////////////////////////////////////////////////////////////////////////
    // source class
    template < typename TInput, typename TSpec >
    struct Pipe< TInput, Source<TSpec> >
    {
        TInput const &in;
        typename Iterator<TInput const, Rooted>::Type cur;
        typename Value<TInput>::Type val;

        Pipe(typename RemoveConst_<TInput>::Type &_cont):
            in(_cont), cur(), val() {}

        Pipe(TInput const &_cont):
            in(_cont), cur(), val() {}

        inline typename Value<TInput>::Type const & operator*()
        { return val = *cur; }

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

    template < typename TInput, typename TSpec, typename TIteratorSpec >
    struct Iterator< Pipe< TInput, Source<TSpec> >, TIteratorSpec> {
        typedef typename Iterator<TInput const, TIteratorSpec>::Type Type;
    };

    template < typename TInput, typename TSpec, typename TTag >
    inline typename Iterator< Pipe< TInput, Source<TSpec> >, Tag<TTag> const >::Type
    begin(Pipe< TInput, Source<TSpec> > &pipe, Tag<TTag> const) {
        return begin(pipe.in);
    }

    template < typename TInput, typename TSpec, typename TTag >
    inline typename Iterator< Pipe< TInput, Source<TSpec> >, Tag<TTag> const >::Type
    end(Pipe< TInput, Source<TSpec> > &pipe, Tag<TTag> const) {
        return end(pipe.in);
    }



    //////////////////////////////////////////////////////////////////////////////
    // simple buffer adaption for fast random accessable containers
    template < typename TContainer >
    struct ContainerBuffer
    {
        TContainer *cont;

        ContainerBuffer(): cont(NULL) {}
        ContainerBuffer(TContainer &_cont): cont(&_cont) {}

        template <typename TSize>
        inline typename Reference<TContainer>::Type
        operator[] (TSize i) {
            return (*cont)[i];
        }
    };

    template < typename TContainer, typename TIteratorSpec >
    struct Iterator< ContainerBuffer<TContainer>, TIteratorSpec>:
        Iterator<TContainer, TIteratorSpec> {};

    template < typename TContainer  >
    struct Value< ContainerBuffer<TContainer> >:
        Value<TContainer> {};

    template < typename TContainer >
    struct Size< ContainerBuffer<TContainer> >:
        Size<TContainer> {};


    template < typename TContainer >
    inline typename Size< ContainerBuffer<TContainer> >::Type
    length(ContainerBuffer<TContainer> const &me) {
        if (me.cont)
            return length(*me.cont);
        else
            return 0;
    }


    //////////////////////////////////////////////////////////////////////////////
    // simple buffer adaption for fast random accessable iterators
    template < typename TIterator >
    struct IteratorBuffer
    {
        TIterator                        begin;
        typename Size<TIterator>::Type    size;

        IteratorBuffer(): begin(NULL), size(0) {}
        template <typename TSize>
        IteratorBuffer(TIterator &_begin, TSize _size): begin(&_begin), size(_size) {}

        template <typename TSize>
        inline typename Reference<TIterator>::Type
        operator[] (TSize i) {
            return *(begin + i);
        }
    };

    template < typename TIterator, typename TIteratorSpec >
    struct Iterator< IteratorBuffer<TIterator>, TIteratorSpec >:
        Iterator<TIterator, TIteratorSpec> {};

    template < typename TIterator  >
    struct Value< IteratorBuffer<TIterator> >:
        Value<TIterator> {};

    template < typename TIterator >
    struct Size< IteratorBuffer<TIterator> >:
        Size<TIterator> {};


    template < typename TIterator >
    inline typename Size< IteratorBuffer<TIterator> >::Type
    length(IteratorBuffer<TIterator> const &me) {
        return me.size;
    }


    //////////////////////////////////////////////////////////////////////////////
    // handler that emulates a buffer by using a container buffer
    struct SourceNonCachingSpec_;
    typedef Tag<SourceNonCachingSpec_> SourceNonCachingSpec;

    template < typename TPipe >
    struct BufferHandler< TPipe, SourceNonCachingSpec >
    {
        typedef typename Source<TPipe>::Type    TSource;
        typedef ContainerBuffer<TSource const>    TBuffer;

        TPipe    &pipe;

        BufferHandler(TPipe &_pipe):
            pipe(_pipe) {}

        template <typename TSize>
        BufferHandler(TPipe &_pipe, TSize):
            pipe(_pipe) {}

        inline TBuffer first() {
            return TBuffer(pipe.in);
        }

        inline TBuffer next() {
            return TBuffer();
        }

        inline void process() {}
        inline void end() {}
        inline void cancel() {}
    };

    template < typename TPipe >
    struct Value< BufferHandler< TPipe, SourceNonCachingSpec > > {
        typedef ContainerBuffer< typename Source<TPipe>::Type const > Type;
    };


    //////////////////////////////////////////////////////////////////////////////
    // caching buffer handler
    struct SourceCachingSpec_;
    typedef Tag<SourceCachingSpec_> SourceCachingSpec;

    template < typename TPipe >
    struct BufferHandler< TPipe, SourceCachingSpec >
    {
        typedef typename Value<TPipe>::Type            TValue;
        typedef typename Size<TPipe>::Type            TSize;

        typedef Buffer<TValue>                              TBuffer;
        typedef IPipeIterator<TPipe>                        ISource;
        typedef typename Iterator<TBuffer, Standard>::Type    ITarget;

        TPipe        &pipe;
        size_t        bufferSize;
        TSize        rest;
        TBuffer        buffer;
        ISource        source;

        BufferHandler(TPipe &_pipe, size_t requestedSize):
            pipe(_pipe),
            bufferSize(requestedSize),
            rest(0) {}

        inline TBuffer& first() {
            rest = length(pipe);
            allocPage(buffer, _min(bufferSize, rest), *this);
            source = ISource(pipe);
            for(ITarget target = buffer.begin; target != buffer.end; ++target) {
                *target = *source;
                ++source;
            }
            if (!(rest -= length(buffer))) source = ISource();
            return buffer;
        }

        inline TBuffer& next() {
            resize(buffer, _min(bufferSize, rest));
            ITarget _end = buffer.begin + length(buffer);
            for(ITarget target = buffer.begin; target != _end; ++target) {
                *target = *source;
                ++source;
            }
            if (!(rest -= length(buffer))) source = ISource();
            return buffer;
        }

        inline void process() {}
        inline void end() { cancel(); }
        inline void cancel() { source = ISource(); freePage(buffer, *this); }
    };

    template < typename TPipe >
    struct Value< BufferHandler< TPipe, SourceCachingSpec > > {
        typedef Buffer<typename Value<TPipe>::Type> Type;
    };

    //////////////////////////////////////////////////////////////////////////////
    // buffer handler optimized for external string sources
    struct ExtStringSourceCachingSpec_;
    typedef Tag<ExtStringSourceCachingSpec_> ExtStringSourceCachingSpec;

    template < typename TSequence, typename TSpec >
    struct BufferHandler< Pipe<TSequence, TSpec>, ExtStringSourceCachingSpec >
    {
        typedef typename Value<TSequence>::Type        TValue;
        typedef typename Size<TSequence>::Type        TSize;
        typedef Buffer<TValue>                      TBuffer;
        typedef Pipe<TSequence, TSpec>                TPipe;

        typedef typename Iterator<TSequence const, Standard>::Type    ISource;
        typedef typename Iterator<TBuffer, Standard>::Type            ITarget;

        TPipe        &pipe;
        unsigned    bufferSize;
        TSize        rest;
        TBuffer        buffer;
        ISource        source;

        BufferHandler(TPipe &_pipe, unsigned requestedSize):
            pipe(_pipe),
            bufferSize(requestedSize),
            rest(0) {}

        inline TBuffer& first() {
            rest = length(pipe.in);
            allocPage(buffer, _min(bufferSize, rest), *this);
            source = begin(pipe.in);
            for(ITarget target = buffer.begin; target != buffer.end; ++target) {
                *target = *source;
                ++source;
            }
            if (!(rest -= length(buffer))) source = ISource();
            return buffer;
        }

        inline TBuffer& next() {
            resize(buffer, _min(bufferSize, rest));
            ITarget _end = buffer.begin + length(buffer);
            for(ITarget target = buffer.begin; target != _end; ++target) {
                *target = *source;
                ++source;
            }
            if (!(rest -= length(buffer))) source = ISource();
            return buffer;
        }

        ~BufferHandler() {
            cancel();
        }

        inline void process() {}
        inline void end() { cancel(); }
        inline void cancel() { source = ISource(); freePage(buffer, *this); }
    };

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

    //////////////////////////////////////////////////////////////////////////////
    // global functions

    // choose the most efficient buffer handler
    template < typename TInput, typename TSpec >
    struct BufReadHandler< Pipe<TInput, TSpec> >
    {
        typedef
            typename IfC<
                AllowsFastRandomAccess<TInput>::VALUE,
                SourceNonCachingSpec,
//                SourceCachingSpec>
                ExtStringSourceCachingSpec >::Type            TTag;
        typedef BufferHandler< Pipe<TInput, TSpec>, TTag>    Type;
    };


    template < typename TValue, typename TConfig, typename TSpec >
    struct BufReadHandler< Pipe< String<TValue, External<TConfig> >, TSpec > >
    {
        typedef BufferHandler<
            Pipe< String<TValue, External<TConfig> >, TSpec >,
            ExtStringSourceCachingSpec
        > Type;
    };

    template < typename TValue, typename TConfig, typename TSpec >
    struct BufReadHandler< Pipe< String<TValue, External<TConfig> > const, TSpec > >
    {
        typedef BufferHandler<
            Pipe< String<TValue, External<TConfig> > const, TSpec >,
            ExtStringSourceCachingSpec
        > Type;
    };


    template < typename TInput, typename TSpec, typename TCommand >
    inline bool control(Pipe< TInput, Source<TSpec> > &/*me*/, TCommand const &)
    {
        return true;
    }

    template < typename TInput, typename TSpec >
    inline bool control(Pipe< TInput, Source<TSpec> > &me, ControlBeginRead const &)
    {
        me.cur = begin(me.in, Rooted());
        return true;
    }

    template < typename TInput, typename TSpec >
    inline bool control(Pipe< TInput, Source<TSpec> > &me, ControlEndRead const &)
    {
        me.cur = end(me.in, Rooted());
        return true;
    }

    template < typename TInput, typename TSpec >
    inline bool control(Pipe< TInput, Source<TSpec> > &me, ControlEof const &)
    {
        return atEnd(me.cur);
    }

    template < typename TInput, typename TSpec >
    inline bool control(Pipe< TInput, Source<TSpec> > &me, ControlEos const &)
    {
        return atEndOfSequence(me.cur);
    }

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

}

#endif
