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// ==========================================================================
// 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: Rene Rahn <rene.rahn@fu-berlin.de>
// ==========================================================================
// Implements the DPCell for affine gap functions. It stores the score
// values for the three matrices: diagonal, vertical and horizontal.
// ==========================================================================
#ifndef SEQAN_INCLUDE_SEQAN_ALIGN_DP_CELL_AFFINE_H_
#define SEQAN_INCLUDE_SEQAN_ALIGN_DP_CELL_AFFINE_H_
namespace seqan2 {
// ============================================================================
// Forwards
// ============================================================================
// ============================================================================
// Tags, Classes, Enums
// ============================================================================
// ----------------------------------------------------------------------------
// Class DPCell [AffineGaps]
// ----------------------------------------------------------------------------
// Specialization for the affine gap cost function.
// This class stores three values belonging to the matrix storing the current
// maximum, the matrix for horizontal gaps and the matrix for vertical gaps.
template <typename TScoreValue>
class DPCell_<TScoreValue, AffineGaps>
{
public:
TScoreValue _score = DPCellDefaultInfinity<DPCell_>::VALUE;
TScoreValue _horizontalScore = DPCellDefaultInfinity<DPCell_>::VALUE;
TScoreValue _verticalScore = DPCellDefaultInfinity<DPCell_>::VALUE;
DPCell_() = default;
// Copy c'tor.
DPCell_(DPCell_<TScoreValue, AffineGaps> const & other) :
_score(other._score),
_horizontalScore(other._horizontalScore),
_verticalScore(other._verticalScore)
{}
// Move c-tor
DPCell_(DPCell_ && other) : DPCell_()
{
swap(*this, other);
}
// The assignment operator.
DPCell_ &
operator=(DPCell_ other)
{
swap(*this, other);
return *this;
}
// Assign score to cell.
DPCell_ &
operator=(TScoreValue const & score)
{
_score = score;
return *this;
}
~DPCell_() = default;
};
// ============================================================================
// Metafunctions
// ============================================================================
// ============================================================================
// Functions
// ============================================================================
// ----------------------------------------------------------------------------
// Function operator<<()
// ----------------------------------------------------------------------------
// Needed for banded chain alignment for the set.
template <typename TStream, typename TScore>
inline TStream& operator<<(TStream & stream,
DPCell_<TScore, AffineGaps> const & dpCell)
{
stream << "<S = " << dpCell._score << " H = " << dpCell._horizontalScore << " V = " << dpCell._verticalScore << ">";
return stream;
}
// ----------------------------------------------------------------------------
// Function operator<()
// ----------------------------------------------------------------------------
// Needed for banded chain alignment for the set.
template <typename TScoreValueLeft, typename TScoreValueRight>
inline bool operator<(DPCell_<TScoreValueLeft, AffineGaps> const & left,
DPCell_<TScoreValueRight, AffineGaps> const & right)
{
return left._score < right._score && left._horizontalScore < right._horizontalScore &&
left._verticalScore < right._verticalScore;
}
// ----------------------------------------------------------------------------
// Function _verticalScoreOfCell()
// ----------------------------------------------------------------------------
// Returns the score of the matrix for vertical-gaps of the given cell.
template <typename TScoreValue>
inline typename Reference<DPCell_<TScoreValue, AffineGaps> >::Type
_verticalScoreOfCell(DPCell_<TScoreValue, AffineGaps> & dpCell)
{
return dpCell._verticalScore;
}
template <typename TScoreValue>
inline typename Reference<DPCell_<TScoreValue, AffineGaps> const>::Type
_verticalScoreOfCell(DPCell_<TScoreValue, AffineGaps> const & dpCell)
{
return dpCell._verticalScore;
}
// ----------------------------------------------------------------------------
// Function _setVerticalScoreOfCell()
// ----------------------------------------------------------------------------
// Returns the score of the matrix for vertical-gaps of the given cell.
template <typename TScoreValue>
inline SEQAN_FUNC_ENABLE_IF(Not<Is<SimdVectorConcept<TScoreValue> > >,void)
_setVerticalScoreOfCell(DPCell_<TScoreValue, AffineGaps> & dpCell, TScoreValue const & newVerticalScore)
{
dpCell._verticalScore = newVerticalScore;
}
template <typename TScoreValue>
inline SEQAN_FUNC_ENABLE_IF(Is<SimdVectorConcept<TScoreValue> >,void)
_setVerticalScoreOfCell(DPCell_<TScoreValue, AffineGaps> & dpCell, TScoreValue const & newVerticalScore)
{
dpCell._verticalScore = newVerticalScore;
}
template <typename TScoreValue>
inline SEQAN_FUNC_ENABLE_IF(Is<SimdVectorConcept<TScoreValue> >,void)
_setVerticalScoreOfCell(DPCell_<TScoreValue, AffineGaps> & dpCell, TScoreValue const & newVerticalScore, TScoreValue const & mask)
{
dpCell._verticalScore = blend(dpCell._verticalScore, newVerticalScore, mask);
}
// ----------------------------------------------------------------------------
// Function _horizontalScoreOfCell()
// ----------------------------------------------------------------------------
// Returns the score of the matrix for horizontal-gaps of the given cell.
template <typename TScoreValue>
inline typename Reference<DPCell_<TScoreValue, AffineGaps> >::Type
_horizontalScoreOfCell(DPCell_<TScoreValue, AffineGaps> & dpCell)
{
return dpCell._horizontalScore;
}
template <typename TScoreValue>
inline typename Reference<DPCell_<TScoreValue, AffineGaps> const>::Type
_horizontalScoreOfCell(DPCell_<TScoreValue, AffineGaps> const & dpCell)
{
return dpCell._horizontalScore;
}
// ----------------------------------------------------------------------------
// Function _setHorizontalScoreOfCell()
// ----------------------------------------------------------------------------
// Returns the score of the matrix for vertical-gaps of the given cell.
template <typename TScoreValue>
inline SEQAN_FUNC_ENABLE_IF(Not<Is<SimdVectorConcept<TScoreValue> > >,void)
_setHorizontalScoreOfCell(DPCell_<TScoreValue, AffineGaps> & dpCell, TScoreValue const & newHorizontalScore)
{
dpCell._horizontalScore = newHorizontalScore;
}
template <typename TScoreValue>
inline SEQAN_FUNC_ENABLE_IF(Is<SimdVectorConcept<TScoreValue> >,void)
_setHorizontalScoreOfCell(DPCell_<TScoreValue, AffineGaps> & dpCell, TScoreValue const & newHorizontalScore)
{
dpCell._horizontalScore = newHorizontalScore;
}
template <typename TScoreValue>
inline SEQAN_FUNC_ENABLE_IF(Is<SimdVectorConcept<TScoreValue> >,void)
_setHorizontalScoreOfCell(DPCell_<TScoreValue, AffineGaps> & dpCell, TScoreValue const & newHorizontalScore, TScoreValue const & mask)
{
dpCell._horizontalScore = blend(dpCell._horizontalScore, newHorizontalScore, mask);
}
template <typename TScoreValue>
inline void
swap(DPCell_<TScoreValue, AffineGaps> & lhs,
DPCell_<TScoreValue, AffineGaps> & rhs)
{
std::swap(lhs._score, rhs._score);
std::swap(lhs._horizontalScore, rhs._horizontalScore);
std::swap(lhs._verticalScore, rhs._verticalScore);
}
} // namespace seqan2
#endif // #ifndef SEQAN_INCLUDE_SEQAN_ALIGN_DP_CELL_AFFINE_H_
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