// ==========================================================================
//                 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
// 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: Manuel Holtgrewe <manuel.holtgrewe@fu-berlin.de>
// ==========================================================================

// TODO(holtgrew): Switch to Host interface.

#ifndef SEQAN_INCLUDE_SEQAN_ALIGN_GAPS_ITERATOR_BASE_H_
#define SEQAN_INCLUDE_SEQAN_ALIGN_GAPS_ITERATOR_BASE_H_

namespace seqan2 {

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

// Internally used tag for creating iterators at the begin of containers.
struct Begin__;
typedef Tag<Begin__> Begin_;

// Internally used tag for creating iterators at the end of containers.
struct End__;
typedef Tag<End__> End_;

// Internally used tag for creating iterators inside of containers.
struct Position__;
typedef Tag<Position__> Position_;

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

/*!
 * @class GapsIterator
 * @implements RandomAccessIteratorConcept
 *
 * @brief Iterator class for @link Gaps @endlink.
 *
 * @signature template <typename TGaps, typename TSpec>
 *            class Iter<TGaps, GapsIterator<TSpec> >;
 *
 * @tparam TGaps The @link Gaps @endlink object for the iterator.
 * @tparam TSpec The specializing tag.
 */

template <typename TSpec>
struct GapsIterator;

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

// ----------------------------------------------------------------------------
// Metafunction Position
// ----------------------------------------------------------------------------

template <typename TGaps, typename TSpec>
struct Position<Iter<TGaps, GapsIterator<TSpec> > > :
            Position<TGaps>
{};

template <typename TGaps, typename TSpec>
struct Position<Iter<TGaps, GapsIterator<TSpec> > const> :
            Position<Iter<TGaps, GapsIterator<TSpec> > >
{};

// ----------------------------------------------------------------------------
// Metafunction Difference
// ----------------------------------------------------------------------------

template <typename TGaps, typename TSpec>
struct Difference<Iter<TGaps, GapsIterator<TSpec> > > :
            Difference<TGaps>
{};

template <typename TGaps, typename TSpec>
struct Difference<Iter<TGaps, GapsIterator<TSpec> > const> :
            Difference<Iter<TGaps, GapsIterator<TSpec> > >
{};

// ----------------------------------------------------------------------------
// Metafunction Source
// ----------------------------------------------------------------------------

// TODO(holtgrew): Should this be Host? or SourceIterator?

template <typename TGaps, typename TSpec>
struct Source<Iter<TGaps, GapsIterator<TSpec> > >
{
    typedef typename Source<TGaps>::Type TSource_;
    typedef typename Iterator<TSource_, Rooted>::Type Type;
};

template <typename TGaps, typename TSpec>
struct Source<Iter<TGaps, GapsIterator<TSpec> > const>
{
    typedef typename Source<TGaps>::Type TSource_;
    typedef typename Iterator<TSource_, Rooted>::Type Type;
};

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

template <typename TGaps, typename TSpec>
struct Value<Iter<TGaps, GapsIterator<TSpec> > >
{
    typedef typename Source<Iter<TGaps, GapsIterator<TSpec> > >::Type TSource_;
    typedef typename Value<TSource_>::Type TSourceValue_;
    //typedef TSourceValue_ Type;
    // TODO(holtgrew): We really want gapped values here but there are issues...
    typedef typename GappedValueType<TSourceValue_>::Type Type;
};

template <typename TGaps, typename TSpec>
struct Value<Iter<TGaps, GapsIterator<TSpec> > const> :
            Value<Iter<TGaps, GapsIterator<TSpec> > > {};

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

template <typename TGaps, typename TSpec>
struct GetValue<Iter<TGaps, GapsIterator<TSpec> > > :
    Value<Iter<TGaps, GapsIterator<TSpec> > >
{
};

template <typename TGaps, typename TSpec>
struct GetValue<Iter<TGaps, GapsIterator<TSpec> > const> :
    Value<Iter<TGaps, GapsIterator<TSpec> > const>
{
};

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

template <typename TGaps, typename TSpec>
struct Reference<Iter<TGaps, GapsIterator<TSpec> > >
{
    typedef Iter<TGaps, GapsIterator<TSpec> > TIterator_;
    typedef Proxy<IteratorProxy<TIterator_> > Type;
};

template <typename TGaps, typename TSpec>
struct Reference<Iter<TGaps, GapsIterator<TSpec> > const>
{
    typedef Iter<TGaps, GapsIterator<TSpec> const > TIterator_;
    typedef Proxy<IteratorProxy<TIterator_> > Type;
};

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

// ----------------------------------------------------------------------------
// Function operator++
// ----------------------------------------------------------------------------

// TODO(holtgrew): Could be general forward

template <typename TGaps, typename TSpec>
inline Iter<TGaps, GapsIterator<TSpec> > &
operator++(Iter<TGaps, GapsIterator<TSpec> > & it)
{
    goNext(it);
    return it;
}

template <typename TGaps, typename TSpec>
inline Iter<TGaps, GapsIterator<TSpec> >
operator++(Iter<TGaps, GapsIterator<TSpec> > & it, int)
{
    Iter<TGaps, GapsIterator<TSpec> > ret = it;
    goNext(it);
    return ret;
}

// ----------------------------------------------------------------------------
// Function operator--
// ----------------------------------------------------------------------------

template <typename TGaps, typename TSpec>
inline Iter<TGaps, GapsIterator<TSpec> > &
operator--(Iter<TGaps, GapsIterator<TSpec> > & it)
{
    goPrevious(it);
    return it;
}

template <typename TGaps, typename TSpec>
inline Iter<TGaps, GapsIterator<TSpec> >
operator--(Iter<TGaps, GapsIterator<TSpec> > & it, int)
{
    Iter<TGaps, GapsIterator<TSpec> > ret = it;
    goPrevious(it);
    return ret;
}

// ----------------------------------------------------------------------------
// Function insertGap()
// ----------------------------------------------------------------------------

/*!
 * @fn GapsIterator#insertGap
 * @brief Insert gap at the current position.
 *
 * @signature void insertGap(it);
 *
 * @param[in,out] it The iterator to insert gaps at.
 */

// Forward to insertGaps() which has to be implemented by the specific gap
// iterator.

template <typename TGaps, typename TSpec>
inline void
insertGap(Iter<TGaps, GapsIterator<TSpec> > & it)
{
    insertGaps(it, 1);
}

// ----------------------------------------------------------------------------
// Function isCharacter()
// ----------------------------------------------------------------------------

/*!
 * @fn GapsIterator#isCharacter
 * @brief Query an iterator for being at a character
 *
 * @signature bool isCharacter(it);
 *
 * @param[in] it Iterator to query for pointing at a character.
 *
 * @return bool <tt>true</tt> if <tt>it</tt> is at a character and <tt>false</tt> otherwise.
 */

template <typename TGaps, typename TSpec>
bool isCharacter(Iter<TGaps, GapsIterator<TSpec> > const & it)
{
    return !isGap(it);
}

// ----------------------------------------------------------------------------
// Function countCharacters()
// ----------------------------------------------------------------------------

/*!
 * @fn GapsIterator#countCharacters
 * @brief Count characters at iterator.
 *
 * @signature TSize countCharacters(it[, dir]);
 *
 * @param[in] it  Iterator for counting characters at.
 * @param[in] dir A tag to specify the counting direction. One of @link GapDirectionTags @endlink.
 *                Defaults to @link GapDirectionTags#RightOfViewPos @endlink.
 *
 * @return TSize Number of characters.
 *
 * If the the direction tag is @link GapDirectionTags#RightOfViewPos @endlink the current view position will be
 * included in the count, and excluded when @link GapDirectionTags#LeftOfViewPos @endlink is selected.
 */

template <typename TGaps, typename TSpec>
inline typename Size<TGaps>::Type
countCharacters(Iter<TGaps, GapsIterator<TSpec> > const & it)
{
    return countCharacters(it, RightOfViewPos());
}

// ----------------------------------------------------------------------------
// Function isGap()
// ----------------------------------------------------------------------------

/*!
 * @fn GapsIterator#isGap
 * @brief Query an iterator for being at a gap
 *
 * @signature bool isGap(it);
 *
 * @param[in] it Iterator to query for pointing at a gap.
 *
 * @return bool <tt>true</tt> if <tt>it</tt> is at a gap and <tt>false</tt> otherwise.
 */

// ----------------------------------------------------------------------------
// Function countGaps()
// ----------------------------------------------------------------------------

/*!
 * @fn GapsIterator#countGaps
 * @brief Count gaps at iterator.
 *
 * @signature TSize countGaps(it[, dir]);
 *
 * @param[in] it Iterator for counting gaps at.
 * @param[in] dir A tag to specify the counting direction. One of @link GapDirectionTags @endlink.
 *                Defaults to @link GapDirectionTags#RightOfViewPos @endlink.
 *
 * @return TSize Number of gaps.
 *
 * If the the direction tag is @link GapDirectionTags#RightOfViewPos @endlink the current view position will be
 * included in the count, and excluded when @link GapDirectionTags#LeftOfViewPos @endlink is selected.
 */

template <typename TGaps, typename TSpec>
inline typename Size<TGaps>::Type
countGaps(Iter<TGaps, GapsIterator<TSpec> > const & it)
{
    return countGaps(it, RightOfViewPos());
}

// ----------------------------------------------------------------------------
// Function insertGaps()
// ----------------------------------------------------------------------------

/*!
 * @fn GapsIterator#insertGaps
 * @brief Insert gaps at the current position.
 *
 * @signature void insertGaps(it, num);
 *
 * @param[in,out] it  Remove gap at the given position (if any).
 * @param[in]     num Number of gaps to insert.
 */

// ----------------------------------------------------------------------------
// Function removeGap()
// ----------------------------------------------------------------------------

/*!
 * @fn GapsIterator#removeGap
 * @brief Insert gap at the current position.
 *
 * @signature TSize removeGap(it);
 *
 * @param[in,out] it Remove gap at the given position (if any).
 *
 * @return TSize Number of removed gaps.
 */

// Forward to removeGaps() which has to be implemented by the specific gap
// iterator.

template <typename TGaps, typename TSpec>
inline typename Size<TGaps>::Type
removeGap(Iter<TGaps, GapsIterator<TSpec> > & it)
{
    return removeGaps(it, 1);
}

// ----------------------------------------------------------------------------
// Function removeGaps()
// ----------------------------------------------------------------------------

/*!
 * @fn GapsIterator#removeGaps
 * @brief Remove gaps from the current position.
 *
 * @signature TSize removeGaps(it, num);
 *
 * @param[in,out] it  Remove gap at the given position (if any).
 * @param[in]     num Number of gaps to remove.
 *
 * @return TSize Number of removed gaps.
 */

// ----------------------------------------------------------------------------
// Function assignValue()
// ----------------------------------------------------------------------------

// TODO(holtgrew): Const consistency problems.

template <typename TGaps, typename TSpec, typename TValue>
inline void
assignValue(Iter<TGaps, GapsIterator<TSpec> > & me,
            TValue const & val)
{
    if (!isGap(me))
    {
        assignValue(source(me), val);
    }
    // TODO(holtgrew): Else, inserting gaps is problematic...
}

template <typename TGaps, typename TSpec, typename TValue>
inline void
assignValue(Iter<TGaps, GapsIterator<TSpec> > const & me,
            TValue const & val)
{
    if (!isGap(me))
    {
        assignValue(source(me), val);
    }
}

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

template <typename TGaps, typename TSpec>
inline TGaps &
container(Iter<TGaps, GapsIterator<TSpec> > & me)
{
    return *me._container;
}

template <typename TGaps, typename TSpec>
inline TGaps &
container(Iter<TGaps, GapsIterator<TSpec> > const & me)
{
    return *me._container;
}

// ----------------------------------------------------------------------------
// Function source
// ----------------------------------------------------------------------------

// Returns host iterator.

// TODO(holtgrew): Non-const version is superfluous.
template <typename TGaps, typename TSpec>
inline typename Source<Iter<TGaps, GapsIterator<TSpec> > >::Type /*returns copy*/
source(Iter<TGaps, GapsIterator<TSpec> > & it)
{
    return iter(container(it), toSourcePosition(container(it), position(it)));
}

template <typename TGaps, typename TSpec>
inline typename Source<Iter<TGaps, GapsIterator<TSpec> > const>::Type /*returns copy*/
source(Iter<TGaps, GapsIterator<TSpec> > const & it)
{
    return iter(container(source(it)), toSourcePosition(container(it), position(it)));
}

// TODO(holtgrew): setSource? setContainer?

// ----------------------------------------------------------------------------
// Function operator+=
// ----------------------------------------------------------------------------

template <typename TGaps, typename TSpec, typename TDiff>
inline Iter<TGaps, GapsIterator<TSpec> > &
operator+=(Iter<TGaps, GapsIterator<TSpec> > & it, TDiff diff)
{
    goFurther(it, diff);
    return it;
}

// ----------------------------------------------------------------------------
// Function operator-=
// ----------------------------------------------------------------------------

template <typename TGaps, typename TSpec, typename TDiff>
inline Iter<TGaps, GapsIterator<TSpec> > &
operator-=(Iter<TGaps, GapsIterator<TSpec> > & it, TDiff diff)
{
    goFurther(it, -(int64_t)(diff));
    return it;
}

// ----------------------------------------------------------------------------
// Function goFurther
// ----------------------------------------------------------------------------

// TODO(holtgrew): Implementation could be faster.
template <typename TGaps, typename TSpec, typename TDifference>
inline void
goFurther(Iter<TGaps, GapsIterator<TSpec> > & it,
          TDifference steps)
{
    typedef typename MakeSigned<TDifference>::Type TSignedDifference;
    if (steps > TDifference(0))
        for (; steps; --steps)
            goNext(it);
    else
        for (; -static_cast<TSignedDifference>(steps); ++steps)
            goPrevious(it);
}

// ----------------------------------------------------------------------------
// Function isClipped()
// ----------------------------------------------------------------------------

template <typename TGaps, typename TSpec>
inline bool
isClipped(Iter<TGaps, GapsIterator<TSpec> > const &)
{
    return false;
}

}  // namespace seqan2

#endif  // SEQAN_INCLUDE_SEQAN_ALIGN_GAPS_ITERATOR_BASE_H_
