// ==========================================================================
//                 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: Andreas Gogol-Doering <andreas.doering@mdc-berlin.de>
// Author: David Weese <david.weese@fu-berlin.de>
// ==========================================================================
// Implementation of the specialization ConcatVirtual of class Iter that
// allows the iteration of arbitrary StringSet objects as if they were
// the concatenation of all strings.
// ==========================================================================

#ifndef SEQAN_SEQUENCE_ITER_CONCAT_VIRTUAL_H_
#define SEQAN_SEQUENCE_ITER_CONCAT_VIRTUAL_H_

namespace seqan {

// ============================================================================
// Forwards
// ============================================================================

// The Metafunction Concatenator is actually defined in string_set_base.h.
template <typename T>
struct Concatenator;

// ============================================================================
// Tags, Classes, Enums
// ============================================================================

template <typename TDelimiter = void >
struct ConcatVirtual;

// TODO(holtgrew): Ask David about objNo and offset.
/**
.Spec.ConcatVirtual Iterator
..cat:Sequences
..general:Class.Iter
..summary:Iterator that sequentially iterates through the elements of a @Class.StringSet@ as if they were directly concatenated, cmp. @Spec.ConcatDirect@.
..signature:Iter<TStringSet, ConcatVirtual<TSpec> >
..param.TStringSet:Type of the @Class.StringSet@.
..param.TSpec:The delimiter to use.
..include:seqan/sequence.h

.Memfunc.ConcatVirtual Iterator#Iter:
..class:Spec.ConcatVirtual Iterator
..summary:Constructor
..signature:Iter(host)
..signature:Iter(host, objNo, offset)
..param.host:Container to iterate.
..param.objNo:Sequence number to set the iterator to.
..param.offset:Offset in the object (specified by objNo) to point to.
..remarks:If $objNo$ and $offset$ are not given, the iterator will point to the first element with offset 0.
 */
template <typename TStringSet, typename TSpec >
class Iter<TStringSet, ConcatVirtual<TSpec> >
{
public:
    typedef typename Value<TStringSet>::Type    TString;
    typedef typename Value<TString>::Type       TValue;
    typedef typename Size<TString>::Type        TSize;

    // TODO(holtgrew): obj_iterator and const_obj_iterator do not appear to be in any C++/STL standard and do not conform to SeqAn's naming scheme.
    typedef typename Iterator<TString, Standard>::Type            obj_iterator;
    typedef typename Iterator<TString const, Standard>::Type      const_obj_iterator;

    // ----------------------------------------------------------------------
    // STL compatible public iterator interface
    typedef Iter                                iterator;
    typedef ::std::bidirectional_iterator_tag   iterator_category;
    typedef TValue                              value_type;
    typedef TValue &                            reference;
    typedef TValue const &                      const_reference;
    typedef TValue *                            pointer;
    typedef TSize                               size_type;
    typedef typename Difference<TString>::Type  difference_type;
    // ----------------------------------------------------------------------

    TStringSet *    host;
    unsigned        objNo;
    obj_iterator    _begin, _cur, _end;

    inline Iter() {}

    inline Iter(TStringSet &_host)
        : host(&_host)
    {
        objNo = 0;
        _begin = _cur = begin(_host[objNo]);
        _end = end(_host[objNo]);
        _testEnd();
    }

    inline Iter(TStringSet &_host, unsigned _objNo, difference_type _offset)
        : host(&_host)
    {
        if (_objNo <length(_host)) {
            objNo = _objNo;
            _begin = _cur = begin(_host[objNo]);
            _end = end(_host[objNo]);
            goFurther(_cur, _offset);
            _testEnd();
        } else {
            objNo = length(_host) - 1;
            _begin = _cur = _end = end(_host[objNo]);
        }
    }

    // ----------------------------------------------------------------------
    // Conversion operators; have to be defined in class def.
    // ----------------------------------------------------------------------

    inline operator obj_iterator()
    {
        return _cur;
    }

    inline operator void * ()
    {
        return _cur;
    }

    // ----------------------------------------------------------------------
    // Shared methods for methods that *have* to be defined in the class def.
    // ----------------------------------------------------------------------

    // _testEnd() is used in the constructors only, so having it here as a
    // non-public function is allowed.
    inline void _testEnd()
    {
        while (_cur == _end && objNo < (length(*host) - 1)) {
            ++objNo;
            _begin = _cur = begin((*host)[objNo]);
            _end = end((*host)[objNo]);
        };
    }
};

// ============================================================================
// Metafunctions
// ============================================================================

// --------------------------------------------------------------------------
// Metafunction Value
// --------------------------------------------------------------------------

template <typename TStringSet, typename TSpec>
struct Value<Iter<TStringSet, ConcatVirtual<TSpec> > >
    : Value<typename Value<TStringSet>::Type> {};

template <typename TStringSet, typename TSpec>
struct Value<Iter<TStringSet, ConcatVirtual<TSpec> > const>
    : Value<typename Value<TStringSet>::Type> {};

// --------------------------------------------------------------------------
// Metafunction GetValue
// --------------------------------------------------------------------------

template <typename TStringSet, typename TSpec>
struct GetValue<Iter<TStringSet, ConcatVirtual<TSpec> > >
    : GetValue<typename Value<TStringSet>::Type> {};

template <typename TStringSet, typename TSpec>
struct GetValue<Iter<TStringSet, ConcatVirtual<TSpec> > const>
    : GetValue<typename Value<TStringSet>::Type> {};

// --------------------------------------------------------------------------
// Metafunction Size
// --------------------------------------------------------------------------

template <typename TStringSet, typename TSpec>
struct Size<Iter<TStringSet, ConcatVirtual<TSpec> > >
    : Size<typename Value<TStringSet>::Type> {};
// Default implementation Size<T const> redirects to non-const variant.

// --------------------------------------------------------------------------
// Metafunction Reference
// --------------------------------------------------------------------------

template <typename TStringSet, typename TSpec>
struct Reference<Iter<TStringSet, ConcatVirtual<TSpec> > >
    : Reference<typename Value<TStringSet>::Type> {};

template <typename TStringSet, typename TSpec>
struct Reference<Iter<TStringSet, ConcatVirtual<TSpec> > const >
    : Reference<typename Value<TStringSet>::Type> {};

// ============================================================================
// Functions
// ============================================================================

// --------------------------------------------------------------------------
// Functions value(), operator*()
// --------------------------------------------------------------------------

template <typename TStringSet, typename TSpec>
inline typename Reference<Iter<TStringSet, ConcatVirtual<TSpec> > const>::Type
value(Iter<TStringSet, ConcatVirtual<TSpec> > const & me)
{
    return *me._cur;
}

template <typename TStringSet, typename TSpec>
inline typename Reference<Iter<TStringSet, ConcatVirtual<TSpec> > >::Type
value(Iter<TStringSet, ConcatVirtual<TSpec> > & me)
{
    return *me._cur;
}

template <typename TStringSet, typename TSpec>
inline typename Reference<Iter<TStringSet, ConcatVirtual<TSpec> > const>::Type
operator*(Iter<TStringSet, ConcatVirtual<TSpec> > const & me)
{
    return *me._cur;
}

template <typename TStringSet, typename TSpec>
inline typename Reference<Iter<TStringSet, ConcatVirtual<TSpec> > >::Type
operator*(Iter<TStringSet, ConcatVirtual<TSpec> > & me)
{
    return *me._cur;
}

// --------------------------------------------------------------------------
// Functions goNext(), operator++()
// --------------------------------------------------------------------------

template <typename TStringSet, typename TSpec>
inline void
goNext(Iter<TStringSet, ConcatVirtual<TSpec> > & me)
{
    ++me._cur;
    me._testEnd();
}

template <typename TStringSet, typename TSpec>
inline Iter<TStringSet, ConcatVirtual<TSpec> > const &
operator++(Iter<TStringSet, ConcatVirtual<TSpec> > & me)
{
    goNext(me);
    return me;
}

template <typename TStringSet, typename TSpec>
inline Iter<TStringSet, ConcatVirtual<TSpec> > const &
operator++(Iter<TStringSet, ConcatVirtual<TSpec> > & me, int)
{
    Iter<TStringSet, ConcatVirtual<TSpec> > before = me;
    goNext(me);
    return before;
}

// --------------------------------------------------------------------------
// Functions goPrevious(), operator++()
// --------------------------------------------------------------------------

template <typename TStringSet, typename TSpec>
inline void
goPrevious(Iter<TStringSet, ConcatVirtual<TSpec> > & me)
{
    while (me._cur == me._begin && me.objNo > 0) {
        --me.objNo;
        me._begin = begin((*me.host)[me.objNo]);
        me._end = me._cur = end((*me.host)[me.objNo]);
    }
    --me._cur;
}

template <typename TStringSet, typename TSpec>
inline Iter<TStringSet, ConcatVirtual<TSpec> > const &
operator--(Iter<TStringSet, ConcatVirtual<TSpec> > & me)
{
    goPrevious(me);
    return me;
}

template <typename TStringSet, typename TSpec>
inline Iter<TStringSet, ConcatVirtual<TSpec> > const &
operator--(Iter<TStringSet, ConcatVirtual<TSpec> > & me, int)
{
    Iter<TStringSet, ConcatVirtual<TSpec> > before = me;
    goPrevious(me);
    return before;
}

// --------------------------------------------------------------------------
// Helper function _tell()
// --------------------------------------------------------------------------

template <typename TStringSet, typename TSpec>
inline typename Size<typename Value<TStringSet>::Type >::Type
_tell(Iter<TStringSet, ConcatVirtual<TSpec> > const & me)
{
    typedef typename Size<typename Value<TStringSet>::Type >::Type TSize;
    typedef Pair<unsigned, TSize> TPair;
    return posGlobalize(TPair(me.objNo, difference(me._begin, me._cur)), stringSetLimits(*me.host));
}

// --------------------------------------------------------------------------
// Function operator+()
// --------------------------------------------------------------------------

template <typename TStringSet, typename TSpec, typename TDelta>
inline Iter<TStringSet, ConcatVirtual<TSpec> >
operator+(Iter<TStringSet, ConcatVirtual<TSpec> > const & me, TDelta delta)
{
    Pair<unsigned, typename Size<typename Value<TStringSet>::Type>::Type> pos;
    posLocalize(pos, _tell(me) + delta, stringSetLimits(*me.host));
    return Iter<TStringSet, ConcatVirtual<TSpec> > (*me.host, getValueI1(pos), getValueI2(pos));
}

template <typename TStringSet, typename TSpec, typename T1, typename T2, typename TCompression>
inline Iter<TStringSet, ConcatVirtual<TSpec> >
operator+(Iter<TStringSet, ConcatVirtual<TSpec> > const & me, Pair<T1, T2, TCompression> delta)
{
    Pair<unsigned, typename Size<typename Value<TStringSet>::Type>::Type> pos;
    posLocalize(pos, _tell(me) + delta, stringSetLimits(*me.host));
    return Iter<TStringSet, ConcatVirtual<TSpec> > (*me.host, getValueI1(pos), getValueI2(pos));
}

// --------------------------------------------------------------------------
// Function operator-()
// --------------------------------------------------------------------------

template <typename TSSetL, typename TSpecL, typename TSSetR, typename TSpecR>
typename Difference<Iter<TSSetL, ConcatVirtual<TSpecL> > >::Type
operator-(
    Iter<TSSetL, ConcatVirtual<TSpecL> > const & L,
    Iter<TSSetR, ConcatVirtual<TSpecR> > const & R)
{
    return _tell(L) - _tell(R);
}

template <typename TStringSet, typename TSpec, typename TDelta>
inline Iter<TStringSet, ConcatVirtual<TSpec> >
operator-(Iter<TStringSet, ConcatVirtual<TSpec> > const & me, TDelta delta)
{
    Pair<unsigned, typename Size<typename Value<TStringSet>::Type>::Type> pos;
    posLocalize(pos, _tell(me) - delta, stringSetLimits(*me.host));
    return Iter<TStringSet, ConcatVirtual<TSpec> > (*me.host, getValueI1(pos), getValueI2(pos));
}

// --------------------------------------------------------------------------
// Function operator==()
// --------------------------------------------------------------------------

template <typename TSSetL, typename TSpecL, typename TSSetR, typename TSpecR>
inline bool
operator==(
    Iter<TSSetL, ConcatVirtual<TSpecL> > const & L,
    Iter<TSSetR, ConcatVirtual<TSpecR> > const & R)
{
    SEQAN_ASSERT(L.host == R.host);
    return L.objNo == R.objNo && L._cur == R._cur;
}

template <typename TSSetL, typename TSpecL, typename TSSetR, typename TSpecR>
inline bool
operator!=(
    Iter<TSSetL, ConcatVirtual<TSpecL> > const & L,
    Iter<TSSetR, ConcatVirtual<TSpecR> > const & R)
{
    SEQAN_ASSERT(L.host == R.host);
    return L.objNo != R.objNo || L._cur != R._cur;
}

// --------------------------------------------------------------------------
// Function operator<()
// --------------------------------------------------------------------------

template <typename TSSetL, typename TSpecL, typename TSSetR, typename TSpecR>
inline bool
operator<(
    Iter<TSSetL, ConcatVirtual<TSpecL> > const & L,
    Iter<TSSetR, ConcatVirtual<TSpecR> > const & R)
{
    SEQAN_ASSERT(L.host == R.host);
    return L.objNo < R.objNo || (L.objNo == R.objNo && L._cur < R._cur);
}

template <typename TSSetL, typename TSpecL, typename TSSetR, typename TSpecR>
inline bool
operator > (
    Iter<TSSetL, ConcatVirtual<TSpecL> > const & L,
    Iter<TSSetR, ConcatVirtual<TSpecR> > const & R)
{
    SEQAN_ASSERT(L.host == R.host);
    return L.objNo > R.objNo || (L.objNo == R.objNo && L._cur > R._cur);
}

// --------------------------------------------------------------------------
// Function container()
// --------------------------------------------------------------------------

template <typename TSSet, typename TSpec>
inline typename Concatenator<TSSet>::Type
container(Iter<TSSet, ConcatVirtual<TSpec> > & me)
{
    return concat(*me.host);
}

template <typename TSSet, typename TSpec>
inline typename Concatenator<TSSet>::Type
container(Iter<TSSet, ConcatVirtual<TSpec> > const & me)
{
    return concat(*me.host);
}

// --------------------------------------------------------------------------
// Function atBegin()
// --------------------------------------------------------------------------

template <typename TSSet, typename TSpec>
inline bool
atBegin(Iter<TSSet, ConcatVirtual<TSpec> > & me)
{
    return me._cur == me._begin && me.objNo == 0;
}

template <typename TSSet, typename TSpec>
inline bool
atBegin(Iter<TSSet, ConcatVirtual<TSpec> > const & me)
{
    return me._cur == me._begin && me.objNo == 0;
}

// --------------------------------------------------------------------------
// Function atEnd()
// --------------------------------------------------------------------------

template <typename TSSet, typename TSpec>
inline bool
atEnd(Iter<TSSet, ConcatVirtual<TSpec> > & me)
{
    return me._cur == me._end && me.objNo == (length(*me.host) - 1);
}

template <typename TSSet, typename TSpec>
inline bool
atEnd(Iter<TSSet, ConcatVirtual<TSpec> > const & me)
{
    return me._cur == me._end && me.objNo == (length(*me.host) - 1);
}

// --------------------------------------------------------------------------
// Function atEndOfSequence()
// --------------------------------------------------------------------------

// TODO(holtgrew): Document Function.atEndOfSequence
// TODO(holtgrew): Specifying a catch-all implementation appears a bit too generous, what about concept checking?

/**
.Function.atEndOfSequence
..summary:Returns true if the iterator is at the end of a sequence.
..cat:sequences
..signature:atEndOfSequence(iter)
..param.iter:Iterator to test.
...type:Class.Iter
..returns:$true$ if the iterator is at the end of a sequence.
...type:nolink:$bool$
..include:seqan/sequence.h
 */
template <typename TIterator>
inline bool
atEndOfSequence(TIterator const & me)
{
    return atEnd(me);
}

template <typename TSSet, typename TSpec>
inline bool
atEndOfSequence(Iter<TSSet, ConcatVirtual<TSpec> > const & me)
{
    if (me._cur == me._begin && me.objNo > 0)
        return true;
    if (me._cur == me._end)
        return true;
    return false;
}

template <typename TIterator>
inline bool
atEndOfSequence(TIterator & me)
{
    return atEndOfSequence(reinterpret_cast<TIterator const &>(me));
}

}  // namespace seqan

#endif  // #ifndef SEQAN_SEQUENCE_ITER_CONCAT_VIRTUAL_H_
