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// ==========================================================================
// SeqAn - The Library for Sequence Analysis
// ==========================================================================
// Copyright (c) 2006-2016, 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>
// ==========================================================================
#ifndef INCLUDE_SEQAN_SCORE_SCORE_SIMD_WRAPPER_H_
#define INCLUDE_SEQAN_SCORE_SCORE_SIMD_WRAPPER_H_
namespace seqan
{
// ============================================================================
// Forwards
// ============================================================================
// ============================================================================
// Tags, Classes, Enums
// ============================================================================
template <typename TScoreSpec>
struct ScoreSimdWrapper;
// ----------------------------------------------------------------------------
// Class Score<SimdWrapper>
// ----------------------------------------------------------------------------
/*!
* @class ScoreSimdWrapper
* @headerfile <seqan/score.h>
* @extends SimpleScore
* @brief A wrapper class to extend score calsses for SIMD usage.
*
* @signature template<typename TScoreVec, typename TScoreSpec>
* class Score<TScoreVec, ScoreSimdWrapper<TScoreSpec> >;
*
* @tparam TScoreVec The simd vector type.
* @tparam TScoreSpec The score type to be wrapped.
*
* Extends a @link SimpleScore @endlink or a @link MatrixScore @endlink for the use with simd vectors.
*/
template <typename TScoreVec, typename TScore>
class Score<TScoreVec, ScoreSimdWrapper<TScore> >
{
public:
using TBaseScoreSpec = typename Spec<TScore>::Type;
// We can be either a SimpleScore or a ScoreMatrix.
TScoreVec data_match = createVector<TScoreVec>(0);
TScoreVec data_mismatch = createVector<TScoreVec>(-1);
TScoreVec data_gap_extend = createVector<TScoreVec>(-1);
TScoreVec data_gap_open = createVector<TScoreVec>(-1);
TScore const * _baseScorePtr; // Only needed for the ScoreMatrix data table.
// Default Constructor.
Score()
{}
// Constructing from base score.
template <typename TScoreVal2, typename TScoreSpec2>
Score(Score<TScoreVal2, TScoreSpec2> const & pScore,
SEQAN_CTOR_ENABLE_IF(And<IsSameType<TScoreSpec2, Simple>, IsSameType<TScoreSpec2, TBaseScoreSpec> >)) :
data_match(createVector<TScoreVec>(scoreMatch(pScore))),
data_mismatch(createVector<TScoreVec>(scoreMismatch(pScore))),
data_gap_extend(createVector<TScoreVec>(scoreGapExtend(pScore))),
data_gap_open(createVector<TScoreVec>(scoreGapOpen(pScore))),
_baseScorePtr(nullptr)
{
ignoreUnusedVariableWarning(dummy);
}
template <typename TScoreVal2, typename TScoreSpec2>
Score(Score<TScoreVal2, TScoreSpec2> const & pScore,
SEQAN_CTOR_ENABLE_IF(And<IsScoreMatrix_<TScoreSpec2>, IsSameType<TScoreSpec2, TBaseScoreSpec> >)) :
data_gap_extend(createVector<TScoreVec>(scoreGapExtend(pScore))),
data_gap_open(createVector<TScoreVec>(scoreGapOpen(pScore))),
_baseScorePtr(&pScore)
{
ignoreUnusedVariableWarning(dummy);
}
};
// ============================================================================
// Metafunctions
// ============================================================================
// ============================================================================
// Functions
// ============================================================================
// ----------------------------------------------------------------------------
// Function score(); SimpleScore Wrapper
// ----------------------------------------------------------------------------
template <typename TValue, typename TScore, typename TSeqHVal, typename TSeqVVal>
inline SEQAN_FUNC_DISABLE_IF(IsScoreMatrix_<TScore>, TValue)
score(Score<TValue, ScoreSimdWrapper<TScore> > const & me, TSeqHVal const & valH, TSeqVVal const & valV)
{
return blend(scoreMismatch(me), scoreMatch(me), cmpEq(valH, valV));
}
// ----------------------------------------------------------------------------
// Function score(); ScoreMatrix Wrapper
// ----------------------------------------------------------------------------
template <unsigned LENGTH>
struct VectorLength_
{};
#define SEQAN_FIXED_VECTOR_FILL_VALUE_IMPL_2(t, d, pos) d[t[1 + pos]], d[t[pos]]
#define SEQAN_FIXED_VECTOR_FILL_VALUE_IMPL_4(t, d, pos) SEQAN_FIXED_VECTOR_FILL_VALUE_IMPL_2(t, d, pos + 2), SEQAN_FIXED_VECTOR_FILL_VALUE_IMPL_2(t, d, pos)
#define SEQAN_FIXED_VECTOR_FILL_VALUE_IMPL_8(t, d, pos) SEQAN_FIXED_VECTOR_FILL_VALUE_IMPL_4(t, d, pos + 4), SEQAN_FIXED_VECTOR_FILL_VALUE_IMPL_4(t, d, pos)
#define SEQAN_FIXED_VECTOR_FILL_VALUE_IMPL_16(t, d, pos) SEQAN_FIXED_VECTOR_FILL_VALUE_IMPL_8(t, d, pos + 8), SEQAN_FIXED_VECTOR_FILL_VALUE_IMPL_8(t, d, pos)
#define SEQAN_FIXED_VECTOR_FILL_VALUE_IMPL_32(t, d, pos) SEQAN_FIXED_VECTOR_FILL_VALUE_IMPL_16(t, d, pos + 16), SEQAN_FIXED_VECTOR_FILL_VALUE_IMPL_16(t, d, pos)
#define SEQAN_FIXED_VECTOR_FILL_VALUE_IMPL_DELEGATE(MACRO, t, d) MACRO(t, d, 0)
#define SEQAN_FIXED_VECTOR_FILL_VALUE_IMPL(t, d, SIZE) SEQAN_FIXED_VECTOR_FILL_VALUE_IMPL_DELEGATE(SEQAN_FIXED_VECTOR_FILL_VALUE_IMPL_##SIZE, t, d)
#define SEQAN_FIXED_VECTOR_FILL_IMPL(SIZE) \
template <typename TTarget, typename TPos, typename TData> \
inline void \
_fixedSizeVectorFill(TTarget & target, \
TPos const & pos, \
TData const & data, \
VectorLength_<SIZE> const & /*scope*/) \
{ \
fillVector(target, SEQAN_FIXED_VECTOR_FILL_VALUE_IMPL(pos, data, SIZE)); \
}
SEQAN_FIXED_VECTOR_FILL_IMPL(2)
SEQAN_FIXED_VECTOR_FILL_IMPL(4)
SEQAN_FIXED_VECTOR_FILL_IMPL(8)
SEQAN_FIXED_VECTOR_FILL_IMPL(16)
SEQAN_FIXED_VECTOR_FILL_IMPL(32)
// TODO(rrahn): We should make the fixedSizeVectorFill the fall back gather interface, if gather is not implemented.
template <typename TValue, typename TScore, typename TVal1, typename TVal2>
inline SEQAN_FUNC_ENABLE_IF(IsScoreMatrix_<TScore>, TValue)
score(Score<TValue, ScoreSimdWrapper<TScore> > const & sc, TVal1 const & val1, TVal2 const & val2)
{
SEQAN_ASSERT(sc._baseScorePtr != nullptr);
#ifdef __AVX2__
return gather(&sc._baseScorePtr->data_tab[0], val1 + val2);
#else
TValue results;
_fixedSizeVectorFill(results, val1 + val2, sc._baseScorePtr->data_tab, VectorLength_<LENGTH<TVal1>::VALUE>());
return results;
#endif
}
}
#endif // #ifndef INCLUDE_SEQAN_SCORE_SCORE_SIMD_WRAPPER_H_
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