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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>
// ==========================================================================
// Defines the recursion formula for the dp-alignment algorithms.
// ==========================================================================
#ifndef SEQAN_INCLUDE_SEQAN_ALIGN_DP_FORMULA_H_
#define SEQAN_INCLUDE_SEQAN_ALIGN_DP_FORMULA_H_
namespace seqan2 {
// ============================================================================
// Forwards
// ============================================================================
// ============================================================================
// Tags, Classes, Enums
// ============================================================================
// ----------------------------------------------------------------------------
// Tag RecursionDirectionDiagonal
// ----------------------------------------------------------------------------
struct RecursionDirectionDiagonal_;
typedef Tag<RecursionDirectionDiagonal_> RecursionDirectionDiagonal;
// ----------------------------------------------------------------------------
// Tag RecursionDirectionHorizontal
// ----------------------------------------------------------------------------
struct RecursionDirectionHorizontal_;
typedef Tag<RecursionDirectionHorizontal_> RecursionDirectionHorizontal;
// ----------------------------------------------------------------------------
// Tag RecursionDirectionVertical
// ----------------------------------------------------------------------------
struct RecursionDirectionVertical_;
typedef Tag<RecursionDirectionVertical_> RecursionDirectionVertical;
// ----------------------------------------------------------------------------
// Tag RecursionDirectionAll
// ----------------------------------------------------------------------------
struct RecursionDirectionAll_;
typedef Tag<RecursionDirectionAll_> RecursionDirectionAll;
// ----------------------------------------------------------------------------
// Tag RecursionDirectionUpperDiagonal
// ----------------------------------------------------------------------------
struct RecursionDirectionUpperDiagonal_;
typedef Tag<RecursionDirectionUpperDiagonal_> RecursionDirectionUpperDiagonal;
// ----------------------------------------------------------------------------
// Tag RecursionDirectionLowerDiagonal
// ----------------------------------------------------------------------------
struct RecursionDirectionLowerDiagonal_;
typedef Tag<RecursionDirectionLowerDiagonal_> RecursionDirectionLowerDiagonal;
// ----------------------------------------------------------------------------
// Tag RecursionDirectionZero
// ----------------------------------------------------------------------------
struct RecursionDirectionZero_;
typedef Tag<RecursionDirectionZero_> RecursionDirectionZero;
// ============================================================================
// Metafunctions
// ============================================================================
// Helper typedef to get the correct score value type from the score-matrix navigator.
template <typename TCellTuple>
using ExtractedScoreValueType_ = std::decay_t<decltype(_scoreOfCell(std::get<0>(std::declval<TCellTuple>())))>;
// A transformation trait to select the correct _maxScore overload for checking against 0 in local alignment.
template <typename TTraceConfig>
struct TraceConfigForLocalAlignment_
{
private:
// If not CompleteTrace then use same type.
template <typename TType>
static auto selectType(TType) -> TType;
// In last check of local alignment always invoke SingleTrace _maxScore overload.
template <typename TGapsPlacement>
static auto selectType(TracebackOn<TracebackConfig_<CompleteTrace, TGapsPlacement>>)
-> TracebackOn<TracebackConfig_<SingleTrace, TGapsPlacement>>;
public:
// The modified type
using Type = decltype(selectType(TTraceConfig{}));
};
// ============================================================================
// Functions
// ============================================================================
template <typename TTarget,
typename TSourceLeft,
typename TSourceRight,
typename TTraceLeft,
typename TTraceRight>
inline SEQAN_FUNC_ENABLE_IF(Not<Is<SimdVectorConcept<TTarget>>>, typename TraceBitMap_<TTarget>::Type)
_maxScore(TTarget & target,
TSourceLeft const & srcLeft,
TSourceRight const & srcRight,
TTraceRight const /**/,
TTraceLeft const /**/,
TracebackOff const & /*tag*/)
{
using std::max;
target = max(static_cast<TTarget>(srcLeft), static_cast<TTarget>(srcRight));
return TraceBitMap_<TTarget>::NONE;
}
template <typename TTarget,
typename TSourceLeft,
typename TSourceRight,
typename TTraceLeft,
typename TTraceRight>
inline SEQAN_FUNC_ENABLE_IF(Is<SimdVectorConcept<TTarget>>, typename TraceBitMap_<TTarget>::Type)
_maxScore(TTarget & target,
TSourceLeft const & srcLeft,
TSourceRight const & srcRight,
TTraceRight const /**/,
TTraceLeft const /**/,
TracebackOff const & /*tag*/)
{
target = max(srcLeft, srcRight);
return TraceBitMap_<TTarget>::NONE;
}
template <typename TTarget,
typename TSourceLeft,
typename TSourceRight,
typename TTraceLeft,
typename TTraceRight,
typename TGapsPlacement>
inline SEQAN_FUNC_ENABLE_IF(Not<Is<SimdVectorConcept<TTarget>>>, typename TraceBitMap_<TTarget>::Type)
_maxScore(TTarget & target,
TSourceLeft const & srcLeft,
TSourceRight const & srcRight,
TTraceLeft const traceLeft,
TTraceRight const traceRight,
TracebackOn<TracebackConfig_<SingleTrace, TGapsPlacement> > const & /*tag*/)
{
return (srcLeft < srcRight)
? (target = srcRight, traceRight)
: (target = srcLeft, traceLeft);
}
template <typename TTarget,
typename TSourceLeft,
typename TSourceRight,
typename TTraceLeft,
typename TTraceRight,
typename TGapsPlacement>
inline SEQAN_FUNC_ENABLE_IF(Is<SimdVectorConcept<TTarget>>, typename TraceBitMap_<TTarget>::Type)
_maxScore(TTarget & target,
TSourceLeft const & srcLeft,
TSourceRight const & srcRight,
TTraceLeft const traceLeft,
TTraceRight const traceRight,
TracebackOn<TracebackConfig_<SingleTrace, TGapsPlacement> > const & /*tag*/)
{
auto cmp = cmpGt(srcRight, srcLeft);
target = blend(srcLeft, srcRight, cmp);
return blend(traceLeft, traceRight, cmp);
}
template <typename TTarget,
typename TSourceLeft,
typename TSourceRight,
typename TTraceLeft,
typename TTraceRight,
typename TGapsPlacement>
inline SEQAN_FUNC_ENABLE_IF(Not<Is<SimdVectorConcept<TTarget>>>, typename TraceBitMap_<TTarget>::Type)
_maxScore(TTarget & target,
TSourceLeft const & srcLeft,
TSourceRight const & srcRight,
TTraceLeft const traceLeft,
TTraceRight const traceRight,
TracebackOn<TracebackConfig_<CompleteTrace, TGapsPlacement> > const & /*tag*/)
{
return (srcLeft == srcRight)
? (target = srcLeft, traceLeft | traceRight)
: (srcLeft < srcRight)
? (target = srcRight, traceRight)
: (target = srcLeft, traceLeft);
}
template <typename TTarget,
typename TSourceLeft,
typename TSourceRight,
typename TTraceLeft,
typename TTraceRight,
typename TGapsPlacement>
inline SEQAN_FUNC_ENABLE_IF(Is<SimdVectorConcept<TTarget>>, typename TraceBitMap_<TTarget>::Type)
_maxScore(TTarget & target,
TSourceLeft const & srcLeft,
TSourceRight const & srcRight,
TTraceLeft const traceLeft,
TTraceRight const traceRight,
TracebackOn<TracebackConfig_<CompleteTrace, TGapsPlacement> > const & /*tag*/)
{
auto cmpG = cmpGt(srcRight, srcLeft);
auto cmpE = cmpEq(srcRight, srcLeft);
target = blend(srcLeft, srcRight, cmpG);
auto result = blend(traceLeft, traceRight, cmpG);
return blend(result, traceLeft | traceRight, cmpE);
}
// ----------------------------------------------------------------------------
// Function _computeScore [RecursionDirectionDiagonal]
// ----------------------------------------------------------------------------
// Independent of gap cost model.
template <typename TScoreValue, typename TGapCosts,
typename TSequenceHValue,
typename TSequenceVValue,
typename TScoringScheme,
typename TAlgorithm, typename TTracebackConfig, typename TExecPolicy>
inline auto
_computeScore(DPCell_<TScoreValue, TGapCosts> & current,
DPCell_<TScoreValue, TGapCosts> & diagonal,
DPCell_<TScoreValue, TGapCosts> const & /*horizontal*/,
DPCell_<TScoreValue, TGapCosts> const & /*vertical*/,
TSequenceHValue const & seqHVal,
TSequenceVValue const & seqVVal,
TScoringScheme const & scoringScheme,
RecursionDirectionDiagonal const &,
DPProfile_<TAlgorithm, TGapCosts, TTracebackConfig, TExecPolicy> const &)
{
_scoreOfCell(current) = _scoreOfCell(diagonal) + score(scoringScheme, seqHVal, seqVVal);
setGapExtension(current, False(), False(), createVector<TScoreValue>(-1));
if (IsLocalAlignment_<TAlgorithm>::VALUE)
{
using TMaxScorePolicy = typename TraceConfigForLocalAlignment_<TTracebackConfig>::Type;
return _maxScore(_scoreOfCell(current),
TraceBitMap_<TScoreValue>::NONE,
_scoreOfCell(current),
TraceBitMap_<TScoreValue>::NONE,
TraceBitMap_<TScoreValue>::DIAGONAL,
TMaxScorePolicy{});
}
else
{
return TraceBitMap_<TScoreValue>::DIAGONAL;
}
}
// ----------------------------------------------------------------------------
// Function _computeScore [RecursionDirectionZero]
// ----------------------------------------------------------------------------
// Independent of gap cost model.
template <typename TScoreValue, typename TGapCosts,
typename TSequenceHValue,
typename TSequenceVValue,
typename TScoringScheme,
typename TAlgoTag, typename TTraceFlag, typename TExecPolicy>
inline auto
_computeScore(DPCell_<TScoreValue, TGapCosts> & current,
DPCell_<TScoreValue, TGapCosts> & diagonal,
DPCell_<TScoreValue, TGapCosts> const & /*horizontal*/,
DPCell_<TScoreValue, TGapCosts> & vertical,
TSequenceHValue const & /*seqHVal*/,
TSequenceVValue const & /*seqVVal*/,
TScoringScheme const & /*scoringScheme*/,
RecursionDirectionZero const &,
DPProfile_<TAlgoTag, TGapCosts, TTraceFlag, TExecPolicy> const &)
{
_scoreOfCell(current) = TraceBitMap_<TScoreValue>::NONE;
_scoreOfCell(diagonal) = _scoreOfCell(current);
_scoreOfCell(vertical) = _scoreOfCell(current);
return TraceBitMap_<TScoreValue>::NONE;
}
} // namespace seqan2
#endif // #ifndef SEQAN_INCLUDE_SEQAN_ALIGN_DP_FORMULA_H_
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