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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 dynamic gap model published in "Dynamic Gaps Selector:
// A Smith Waterman Sequence Alignment Algorithm with Affine Gap Model
// Optimization" by Gianvito Urgese et al.
// ==========================================================================
#ifndef INCLUDE_SEQAN_ALIGN_DP_CELL_DYNAMIC_H_
#define INCLUDE_SEQAN_ALIGN_DP_CELL_DYNAMIC_H_
namespace seqan2 {
// ============================================================================
// Forwards
// ============================================================================
// ----------------------------------------------------------------------------
// Metafunction GetFlagMaskType
// ----------------------------------------------------------------------------
namespace impl
{
namespace dp_cell
{
template <typename TScoreValue>
struct FlagMaskType
{
using Type = typename If<Is<SimdVectorConcept<TScoreValue> >,
TScoreValue,
uint8_t>::Type;
};
} // namespace dp_cell
} // namespace impl
// ============================================================================
// Tags, Classes, Enums
// ============================================================================
enum DynamicGapsMask
{
MASK_VERTICAL_GAP = 1,
MASK_HORIZONTAL_GAP = 2
};
// ----------------------------------------------------------------------------
// Class DPCell [DynamicGaps]
// ----------------------------------------------------------------------------
// The specialization for linear gap cost function.
// It solely stores the maximal score.
template <typename TScoreValue>
class DPCell_<TScoreValue, DynamicGaps>
{
public:
using TFlagMaskType = typename impl::dp_cell::FlagMaskType<TScoreValue>::Type;
TScoreValue _score = DPCellDefaultInfinity<DPCell_>::VALUE;
TFlagMaskType _flagMask = TFlagMaskType();
DPCell_() = default;
// Copy c'tor.
DPCell_(DPCell_ const & other) : _score(other._score), _flagMask(other._flagMask)
{}
// Move c'tor.
DPCell_(DPCell_ && other) : DPCell_()
{
swap(*this, other);
}
// Construct with score.
DPCell_(TScoreValue const & pScore) : _score(pScore)
{}
// Assignment and move operator.
DPCell_& operator=(DPCell_ other)
{
swap(*this, other);
return *this;
}
// Assignment of score.
DPCell_ &
operator=(TScoreValue const & score)
{
_score = score;
return *this;
}
~DPCell_() = default;
};
// ============================================================================
// Metafunctions
// ============================================================================
template <typename TCell, typename TBoolV, typename TBoolH>
struct SetGapExtension;
template <typename TScoreValue>
struct SetGapExtension<DPCell_<TScoreValue, DynamicGaps>, False, False>
{
static const char VALUE = 0;
};
template <typename TScoreValue>
struct SetGapExtension<DPCell_<TScoreValue, DynamicGaps>, False, True>
{
static const char VALUE = MASK_HORIZONTAL_GAP;
};
template <typename TScoreValue>
struct SetGapExtension<DPCell_<TScoreValue, DynamicGaps>, True, False>
{
static const char VALUE = MASK_VERTICAL_GAP;
};
template <typename TScoreValue>
struct SetGapExtension<DPCell_<TScoreValue, DynamicGaps>, True, True>
{
static const char VALUE = MASK_HORIZONTAL_GAP | MASK_VERTICAL_GAP;
};
// ============================================================================
// Functions
// ============================================================================
template <typename TScoreValue, typename TFlag>
inline void _setBit(DPCell_<TScoreValue, DynamicGaps> & cell,
TFlag const & /*flag*/,
DynamicGapExtensionVertical const & /*tag*/)
{
SEQAN_IF_CONSTEXPR (IsSameType<TFlag, True>::VALUE)
cell._flagMask |= MASK_VERTICAL_GAP;
else
cell._flagMask &= ~MASK_VERTICAL_GAP;
}
template <typename TScoreValue, typename TFlag>
inline void _setBit(DPCell_<TScoreValue, DynamicGaps> & cell,
TFlag const & /*flag*/,
DynamicGapExtensionHorizontal const & /*tag*/)
{
SEQAN_IF_CONSTEXPR (IsSameType<TFlag, True>::VALUE)
cell._flagMask |= MASK_HORIZONTAL_GAP;
else
cell._flagMask &= ~MASK_HORIZONTAL_GAP;
}
template <typename TScoreValue, typename TSpec>
inline SEQAN_FUNC_ENABLE_IF(Not<Is<SimdVectorConcept<TScoreValue> > >,bool)
isGapExtension(DPCell_<TScoreValue, DynamicGaps> const & cell,
TSpec const & /*spec*/)
{
bool result;
SEQAN_IF_CONSTEXPR (IsSameType<TSpec, DynamicGapExtensionHorizontal>::VALUE)
result = cell._flagMask & MASK_HORIZONTAL_GAP;
else
result = cell._flagMask & MASK_VERTICAL_GAP;
return result;
}
template <typename TScoreValue, typename TSpec>
inline SEQAN_FUNC_ENABLE_IF(Is<SimdVectorConcept<TScoreValue> >,TScoreValue)
isGapExtension(DPCell_<TScoreValue, DynamicGaps> const & cell,
TSpec const & /*spec*/)
{
return blend(cell._flagMask & createVector<TScoreValue>(MASK_VERTICAL_GAP),
cell._flagMask & createVector<TScoreValue>(MASK_HORIZONTAL_GAP),
createVector<TScoreValue>(IsSameType<TSpec, DynamicGapExtensionHorizontal>::VALUE));
}
template <typename TScoreValue, typename TFlagV, typename TFlagH>
inline SEQAN_FUNC_ENABLE_IF(Not<Is<SimdVectorConcept<TScoreValue> > >, void)
setGapExtension(DPCell_<TScoreValue, DynamicGaps> & cell,
TFlagV const & /*vert*/, TFlagH const & /*hori*/)
{
cell._flagMask = SetGapExtension<DPCell_<TScoreValue, DynamicGaps>, TFlagV, TFlagH>::VALUE;
}
template <typename TScoreValue, typename TFlagV, typename TFlagH>
inline SEQAN_FUNC_ENABLE_IF(Is<SimdVectorConcept<TScoreValue> >, void)
setGapExtension(DPCell_<TScoreValue, DynamicGaps> & cell,
TFlagV const & /*vert*/, TFlagH const & /*hori*/,
TScoreValue const & cmp)
{
cell._flagMask = blend(cell._flagMask, createVector<TScoreValue>(SetGapExtension<DPCell_<TScoreValue, DynamicGaps>, TFlagV, TFlagH>::VALUE), cmp);
}
// ----------------------------------------------------------------------------
// Function operator<()
// ----------------------------------------------------------------------------
// Needed for banded chain alignment for the std::set.
template <typename TScoreValueLeft, typename TScoreValueRight>
inline bool operator<(DPCell_<TScoreValueLeft, DynamicGaps> const & left,
DPCell_<TScoreValueRight, DynamicGaps> const & right)
{
return left._score < right._score;
}
template <typename TScoreValue>
inline void
swap(DPCell_<TScoreValue, DynamicGaps> & lhs,
DPCell_<TScoreValue, DynamicGaps> & rhs)
{
std::swap(lhs._score, rhs._score);
std::swap(lhs._flagMask, rhs._flagMask);
}
} // namespace seqan2
#endif // INCLUDE_SEQAN_ALIGN_DP_CELL_DYNAMIC_H_
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