// ==========================================================================
//                 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"
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// OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH
// DAMAGE.
//
// ==========================================================================
// Author: Rene Rahn <rene.rahn@fu-berlin.de>
// ==========================================================================
// Declares the DPCell, which is used to substitute the score of each cell.
// Thus, we are able to add additional features to an alignment cell such as
// a flag to indicate if it is forbidden or not. Or to store two additional
// scores necessary for the affine gap function.
// ==========================================================================

#ifndef SEQAN_INCLUDE_SEQAN_ALIGN_DP_CELL_H_
#define SEQAN_INCLUDE_SEQAN_ALIGN_DP_CELL_H_

namespace seqan2 {

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

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

struct DynamicGapExtensionHorizontal_;
typedef Tag<DynamicGapExtensionHorizontal_> DynamicGapExtensionHorizontal;

struct DynamicGapExtensionVertical_;
typedef Tag<DynamicGapExtensionVertical_> DynamicGapExtensionVertical;

// ----------------------------------------------------------------------------
// Class DPCell_
// ----------------------------------------------------------------------------

// Used to store the score of a particular cell of the score matrix.
// It can be specialized for linear and affine gap costs.
// For affine gap costs it stores the values of all three matrices at a particular
// position of the matrix.
template <typename TScoreValue, typename TGapCosts>
class DPCell_;

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

// ----------------------------------------------------------------------------
// Metafunction Spec
// ----------------------------------------------------------------------------

template <typename TScoreValue, typename TGapCostFunction>
struct Spec<DPCell_<TScoreValue, TGapCostFunction> >
{
    typedef TGapCostFunction Type;
};

template <typename TScoreValue, typename TGapCostFunction>
struct Spec<DPCell_<TScoreValue, TGapCostFunction> const> :
    Spec<DPCell_<TScoreValue, TGapCostFunction> >
{};

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

template <typename TScoreValue, typename TGapCostFunction>
struct Value<DPCell_<TScoreValue, TGapCostFunction> >
{
    typedef TScoreValue Type;
};

template <typename TScoreValue, typename TGapCostFunction>
struct Value<DPCell_<TScoreValue, TGapCostFunction> const>
{
    typedef TScoreValue const Type;
};

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

template <typename TScoreValue, typename TGapCostFunction>
struct Reference<DPCell_<TScoreValue, TGapCostFunction> >
{
    typedef TScoreValue & Type;
};

template <typename TScoreValue, typename TGapCostFunction>
struct Reference<DPCell_<TScoreValue, TGapCostFunction> const>
{
    typedef TScoreValue const & Type;
};

// ----------------------------------------------------------------------------
// Metafunction DPCellDefaultInfinity
// ----------------------------------------------------------------------------

// Defines the default infinity value for a DPCell.
template <typename T>
struct DPCellDefaultInfinity
{
    static const typename Value<T>::Type VALUE;
};

template <typename T>
const typename Value<T>::Type DPCellDefaultInfinity<T>::VALUE = std::numeric_limits<typename Value<T>::Type>::lowest();

// We use the min value of the score type and shift it one bits to the left.  This way we can use "infinity" without
// checking for it during the computation.
template <typename TScoreValue, typename TGapCostFunction>
struct DPCellDefaultInfinity<DPCell_<TScoreValue, TGapCostFunction> >
{
    static const TScoreValue VALUE;
};

template <typename TScoreValue, typename TGapCostFunction>
    const TScoreValue DPCellDefaultInfinity<DPCell_<TScoreValue, TGapCostFunction> >::VALUE =
        createVector<TScoreValue>(std::numeric_limits<typename Value<TScoreValue>::Type>::lowest()) /
        createVector<TScoreValue>(static_cast<typename Value<TScoreValue>::Type>(2));

template <typename TScoreValue, typename TGapCostFunction>
struct DPCellDefaultInfinity<DPCell_<TScoreValue, TGapCostFunction> const> :
    public DPCellDefaultInfinity<DPCell_<TScoreValue, TGapCostFunction> >{};

// ----------------------------------------------------------------------------
// Metafunction StringSpecForValue_
// ----------------------------------------------------------------------------

// Defines the default infinity value for a DPCell.
template <typename TValue, typename TSpec>
struct StringSpecForValue_<DPCell_<TValue, TSpec> >
{
    typedef typename If<Is<SimdVectorConcept<TValue> >, Alloc<OverAligned>, Alloc<> >::Type Type;
};

template <typename TValue, typename TSpec>
struct StringSpecForValue_<DPCell_<TValue, TSpec> const> :
    StringSpecForValue_<DPCell_<TValue, TSpec> >
{};

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

// ----------------------------------------------------------------------------
// Function _scoreOfCell
// ----------------------------------------------------------------------------

// Returns the score value for a given cell.
template <typename TScoreValue, typename TGapCosts>
inline typename Reference<DPCell_<TScoreValue, TGapCosts> >::Type
_scoreOfCell(DPCell_<TScoreValue, TGapCosts> & dpCell)
{
    return dpCell._score;
}

template <typename TScoreValue, typename TGapCosts>
inline typename Reference<DPCell_<TScoreValue, TGapCosts> const>::Type
_scoreOfCell(DPCell_<TScoreValue, TGapCosts> const & dpCell)
{
    return dpCell._score;
}

// ----------------------------------------------------------------------------
// Function _setScoreOfCell
// ----------------------------------------------------------------------------

template <typename TScoreValue, typename TGapCosts>
inline void
_setScoreOfCell(DPCell_<TScoreValue, TGapCosts> & dpCell, TScoreValue const & newScore)
{
    dpCell._score = newScore;
}

template <typename TScoreValue, typename TGapCosts, typename TMask>
inline void
_setScoreOfCell(DPCell_<TScoreValue, TGapCosts> & dpCell, TScoreValue const & newScore)
{
    dpCell._score = newScore;
}

template <typename TScoreValue, typename TGapCosts, typename TMask>
inline void
_setScoreOfCell(DPCell_<TScoreValue, TGapCosts> & dpCell, TScoreValue const & newScore, TMask const & mask)
{
    dpCell._score = blend(dpCell._score, newScore, mask);
}

// ----------------------------------------------------------------------------
// Function _verticalScoreOfCell()
// ----------------------------------------------------------------------------

// Returns the score of the matrix for vertical-gaps of the given cell.
template <typename TScoreValue, typename TGapSpec>
inline typename  Reference<DPCell_<TScoreValue, TGapSpec> >::Type
_verticalScoreOfCell(DPCell_<TScoreValue, TGapSpec> & dpCell)
{
    return dpCell._score;
}

template <typename TScoreValue, typename TGapSpec>
inline typename  Reference<DPCell_<TScoreValue, TGapSpec> const>::Type
_verticalScoreOfCell(DPCell_<TScoreValue, TGapSpec> const & dpCell)
{
    return dpCell._score;
}

// ----------------------------------------------------------------------------
// Function _setVerticalScoreOfCell()
// ----------------------------------------------------------------------------

// Returns the score of the matrix for vertical-gaps of the given cell.
template <typename TScoreValue, typename TGapSpec>
inline void
_setVerticalScoreOfCell(DPCell_<TScoreValue, TGapSpec> & /*dpCell*/, TScoreValue const & /*newVerticalScore*/)
{
    // no-op
}

template <typename TScoreValue, typename TGapSpec, typename TMask>
inline void
_setVerticalScoreOfCell(DPCell_<TScoreValue, TGapSpec> & /*dpCell*/, TScoreValue const & /*newVerticalScore*/, TMask const & /*mask*/)
{
    // no-op
}

// ----------------------------------------------------------------------------
// Function _horizontalScoreOfCell()
// ----------------------------------------------------------------------------

// Returns the score of the matrix for horizontal-gaps of the given cell.
template <typename TScoreValue, typename TGapSpec>
inline typename  Reference<DPCell_<TScoreValue, TGapSpec> >::Type
_horizontalScoreOfCell(DPCell_<TScoreValue, TGapSpec> & dpCell)
{
    return dpCell._score;
}

template <typename TScoreValue, typename TGapSpec>
inline typename  Reference<DPCell_<TScoreValue, TGapSpec> const>::Type
_horizontalScoreOfCell(DPCell_<TScoreValue, TGapSpec> const & dpCell)
{
    return dpCell._score;
}

// ----------------------------------------------------------------------------
// Function _setHorizontalScoreOfCell()
// ----------------------------------------------------------------------------

// Returns the score of the matrix for vertical-gaps of the given cell.
template <typename TScoreValue, typename TGapSpec>
inline void
_setHorizontalScoreOfCell(DPCell_<TScoreValue, TGapSpec> & /*dpCell*/, TScoreValue const & /*newHorizontalScore*/)
{
    // no-op
}

template <typename TScoreValue, typename TGapSpec, typename TMask>
inline void
_setHorizontalScoreOfCell(DPCell_<TScoreValue, TGapSpec> & /*dpCell*/, TScoreValue const & /*newHorizontalScore*/, TMask const & /*mask*/)
{
    // no-op
}

// ----------------------------------------------------------------------------
// Function setGapExtension()
// ----------------------------------------------------------------------------

template <typename TScoreValue, typename TGapSpec, typename TF1, typename TF2>
inline void
setGapExtension(DPCell_<TScoreValue, TGapSpec> & /*dpCell*/, TF1 , TF2)
{
    // no-op
}

template <typename TScoreValue, typename TGapSpec, typename TF1, typename TF2, typename TMask>
inline void
setGapExtension(DPCell_<TScoreValue, TGapSpec> & /*dpCell*/, TF1 , TF2, TMask)
{
    // no-op
}

template <typename TTarget, typename TScoreValue, typename TGapSpec>
inline void
write(TTarget & target, DPCell_<TScoreValue, TGapSpec> const & cell)
{
    write(target, _scoreOfCell(cell));
}

// ----------------------------------------------------------------------------
// Function isGapExtension()
// ----------------------------------------------------------------------------

template <typename TScoreValue, typename TGapSpec,
          typename TSpec>
inline bool
isGapExtension(DPCell_<TScoreValue, TGapSpec> const & /*cell*/,
               TSpec const & /*spec*/)
{
    return false;
}

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

template <typename TScoreValue, typename TGapCosts>
inline bool operator==(DPCell_<TScoreValue, TGapCosts> const & lhs,
                       DPCell_<TScoreValue, TGapCosts> const & rhs)
{
    return _scoreOfCell(lhs) == _scoreOfCell(rhs) &&
           _horizontalScoreOfCell(lhs) == _horizontalScoreOfCell(rhs) &&
           _verticalScoreOfCell(lhs) == _verticalScoreOfCell(rhs);
}

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

template <typename TScoreValue, typename TGapCosts>
inline bool operator!=(DPCell_<TScoreValue, TGapCosts> const & lhs,
                       DPCell_<TScoreValue, TGapCosts> const & rhs)
{
    return !(lhs == rhs);
}

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

template <typename TStream,
          typename TScoreValue, typename TGapCosts>
inline TStream& operator<<(TStream & stream,
                           DPCell_<TScoreValue, TGapCosts> const & cell)
{
    stream << "M: " << _scoreOfCell(cell);
    if (std::is_same<TGapCosts, AffineGaps>::value)
    {
        stream << " <H: " << _horizontalScoreOfCell(cell) << " V: " << _verticalScoreOfCell(cell) << ">";
    }
    else if (std::is_same<TGapCosts, DynamicGaps>::value)
    {
        stream << " <H: " << isGapExtension(cell, DynamicGapExtensionHorizontal{}) <<
                  " V: " << isGapExtension(cell, DynamicGapExtensionVertical{}) << ">";
    }
    return stream;
}

}  // namespace seqan2

#endif  // #ifndef SEQAN_INCLUDE_SEQAN_ALIGN_DP_CELL_H_