// ==========================================================================
// SeqAn - The Library for Sequence Analysis
// ==========================================================================
// Copyright (c) 2006-2018, 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
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// DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
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// DAMAGE.
//
// ==========================================================================
// Author: Rene Rahn <rene.rahn@fu-berlin.de>
// ==========================================================================
// Implements the affine gap cost functions.
// ==========================================================================
#ifndef SEQAN_INCLUDE_SEQAN_ALIGN_DP_FORMULA_AFFINE_H_
#define SEQAN_INCLUDE_SEQAN_ALIGN_DP_FORMULA_AFFINE_H_
namespace seqan {
// ============================================================================
// Forwards
// ============================================================================
// ============================================================================
// Tags, Classes, Enums
// ============================================================================
// ============================================================================
// Metafunctions
// ============================================================================
// ============================================================================
// Functions
// ============================================================================
// ----------------------------------------------------------------------------
// Function _computeScore [RecursionAllDirection, AffineGaps]
// ----------------------------------------------------------------------------
template <typename TScoreValue,
typename TSequenceHValue, typename TSequenceVValue, typename TScoringScheme,
typename TAlgorithm, typename TTracebackConfig, typename TExecPolicy>
inline typename TraceBitMap_<TScoreValue>::Type
_computeScore(DPCell_<TScoreValue, AffineGaps> & current,
DPCell_<TScoreValue, AffineGaps> & previousDiagonal,
DPCell_<TScoreValue, AffineGaps> const & previousHorizontal,
DPCell_<TScoreValue, AffineGaps> & previousVertical,
TSequenceHValue const & seqHVal,
TSequenceVValue const & seqVVal,
TScoringScheme const & scoringScheme,
RecursionDirectionAll const &,
DPProfile_<TAlgorithm, AffineGaps, TTracebackConfig, TExecPolicy> const &)
{
// Compute intermediate diagonal result.
TScoreValue intermediate = static_cast<TScoreValue>(_scoreOfCell(previousDiagonal) +
score(scoringScheme, seqHVal, seqVVal));
// Cache previous Diagonal
_scoreOfCell(previousDiagonal) = _scoreOfCell(previousHorizontal);
// Compute horizontal direction.
auto tmp = _maxScore(_horizontalScoreOfCell(current),
_horizontalScoreOfCell(previousHorizontal) +
scoreGapExtendHorizontal(scoringScheme, seqHVal, seqVVal),
_scoreOfCell(previousHorizontal) +
scoreGapOpenHorizontal(scoringScheme, seqHVal, seqVVal),
TraceBitMap_<TScoreValue>::HORIZONTAL,
TraceBitMap_<TScoreValue>::HORIZONTAL_OPEN,
TTracebackConfig{});
// Compute vertical direction.
tmp |= _maxScore(_verticalScoreOfCell(previousVertical),
_verticalScoreOfCell(previousVertical) +
scoreGapExtendVertical(scoringScheme, seqHVal, seqVVal),
_scoreOfCell(previousVertical) +
scoreGapOpenVertical(scoringScheme, seqHVal, seqVVal),
TraceBitMap_<TScoreValue>::VERTICAL,
TraceBitMap_<TScoreValue>::VERTICAL_OPEN,
TTracebackConfig{});
auto tmp2 = _maxScore(_scoreOfCell(current),
_verticalScoreOfCell(previousVertical),
_horizontalScoreOfCell(current),
TraceBitMap_<TScoreValue>::MAX_FROM_VERTICAL_MATRIX,
TraceBitMap_<TScoreValue>::MAX_FROM_HORIZONTAL_MATRIX,
TTracebackConfig{});
tmp = _maxScore(_scoreOfCell(current),
intermediate,
_scoreOfCell(current),
TraceBitMap_<TScoreValue>::DIAGONAL | tmp,
tmp2 | tmp,
TTracebackConfig{});
if (IsLocalAlignment_<TAlgorithm>::VALUE)
{
tmp = _maxScore(_scoreOfCell(current),
TraceBitMap_<TScoreValue>::NONE,
_scoreOfCell(current),
TraceBitMap_<TScoreValue>::NONE,
tmp,
TTracebackConfig{});
}
// Cache score for previous vertical.
_scoreOfCell(previousVertical) = _scoreOfCell(current);
return tmp;
}
// ----------------------------------------------------------------------------
// Function _computeScore [RecursionUpperDiagonalDirection, AffineGaps]
// ----------------------------------------------------------------------------
template <typename TScoreValue,
typename TSequenceHValue, typename TSequenceVValue, typename TScoringScheme,
typename TAlgorithm, typename TTracebackConfig, typename TExecPolicy>
inline typename TraceBitMap_<TScoreValue>::Type
_computeScore(DPCell_<TScoreValue, AffineGaps> & current,
DPCell_<TScoreValue, AffineGaps> & previousDiagonal,
DPCell_<TScoreValue, AffineGaps> const & previousHorizontal,
DPCell_<TScoreValue, AffineGaps> & previousVertical,
TSequenceHValue const & seqHVal,
TSequenceVValue const & seqVVal,
TScoringScheme const & scoringScheme,
RecursionDirectionUpperDiagonal const &,
DPProfile_<TAlgorithm, AffineGaps, TTracebackConfig, TExecPolicy> const &)
{
typedef typename TraceBitMap_<TScoreValue>::Type TTraceValue;
// Compute intermediate diagonal result.
TScoreValue intermediate = static_cast<TScoreValue>(_scoreOfCell(previousDiagonal) +
score(scoringScheme, seqHVal, seqVVal));
// Cache previous Diagonal
_scoreOfCell(previousDiagonal) = _scoreOfCell(previousHorizontal);
// Compute horiztonal direction.
// _horizontalScoreOfCell(current) = _horizontalScoreOfCell(previousHorizontal) +
// scoreGapExtendHorizontal(scoringScheme, seqHVal, seqVVal);
TTraceValue tv = _maxScore(_horizontalScoreOfCell(current),
_horizontalScoreOfCell(previousHorizontal) +
scoreGapExtendHorizontal(scoringScheme, seqHVal, seqVVal),
_scoreOfCell(previousHorizontal) +
scoreGapOpenHorizontal(scoringScheme, seqHVal, seqVVal),
TraceBitMap_<TScoreValue>::HORIZONTAL,
TraceBitMap_<TScoreValue>::HORIZONTAL_OPEN,
TTracebackConfig());
// Ignore vertical direction in upper diagonal.
_verticalScoreOfCell(previousVertical) = DPCellDefaultInfinity<DPCell_<TScoreValue, AffineGaps> >::VALUE;
// Compute diagonal direction and compare with horizontal.
// _scoreOfCell(current) = _horizontalScoreOfCell(current);
tv = _maxScore(_scoreOfCell(current),
intermediate,
_horizontalScoreOfCell(current),
tv | TraceBitMap_<TScoreValue>::DIAGONAL,
tv | TraceBitMap_<TScoreValue>::MAX_FROM_HORIZONTAL_MATRIX,
TTracebackConfig());
if (IsLocalAlignment_<TAlgorithm>::VALUE)
{
tv = _maxScore(_scoreOfCell(current),
TraceBitMap_<TScoreValue>::NONE,
_scoreOfCell(current),
TraceBitMap_<TScoreValue>::NONE,
tv,
TTracebackConfig{});
}
_scoreOfCell(previousVertical) = _scoreOfCell(current);
return tv;
}
// ----------------------------------------------------------------------------
// Function _computeScore [RecursionDirectionLowerDiagonal, AffineGaps]
// ----------------------------------------------------------------------------
template <typename TScoreValue,
typename TSequenceHValue, typename TSequenceVValue, typename TScoringScheme,
typename TAlgorithm, typename TTracebackConfig, typename TExecPolicy>
inline typename TraceBitMap_<TScoreValue>::Type
_computeScore(DPCell_<TScoreValue, AffineGaps> & current,
DPCell_<TScoreValue, AffineGaps> const & previousDiagonal,
DPCell_<TScoreValue, AffineGaps> const & /*previousHorizontal*/,
DPCell_<TScoreValue, AffineGaps> & previousVertical,
TSequenceHValue const & seqHVal,
TSequenceVValue const & seqVVal,
TScoringScheme const & scoringScheme,
RecursionDirectionLowerDiagonal const &,
DPProfile_<TAlgorithm, AffineGaps, TTracebackConfig, TExecPolicy> const &)
{
typedef typename TraceBitMap_<TScoreValue>::Type TTraceValue;
// Compute vertical direction.
TTraceValue tv = _maxScore(_verticalScoreOfCell(previousVertical),
_verticalScoreOfCell(previousVertical) +
scoreGapExtendVertical(scoringScheme, seqHVal, seqVVal),
_scoreOfCell(previousVertical) +
scoreGapOpenVertical(scoringScheme, seqHVal, seqVVal),
TraceBitMap_<TScoreValue>::VERTICAL,
TraceBitMap_<TScoreValue>::VERTICAL_OPEN,
TTracebackConfig());
// Ignore horizontal direction in lower diagonal.
_horizontalScoreOfCell(current) = DPCellDefaultInfinity<DPCell_<TScoreValue, AffineGaps> >::VALUE;
// Compute diagonal direction and compare with vertical.
tv = _maxScore(_scoreOfCell(current),
_scoreOfCell(previousDiagonal) + score(scoringScheme, seqHVal, seqVVal),
_verticalScoreOfCell(previousVertical),
tv | TraceBitMap_<TScoreValue>::DIAGONAL,
tv | TraceBitMap_<TScoreValue>::MAX_FROM_VERTICAL_MATRIX,
TTracebackConfig());
if (IsLocalAlignment_<TAlgorithm>::VALUE)
{
tv = _maxScore(_scoreOfCell(current),
TraceBitMap_<TScoreValue>::NONE,
_scoreOfCell(current),
TraceBitMap_<TScoreValue>::NONE,
tv,
TTracebackConfig{});
}
return tv;
}
// ----------------------------------------------------------------------------
// Function _computeScore [RecursionHorizontalDirection]
// ----------------------------------------------------------------------------
template <typename TScoreValue,
typename TSequenceHValue, typename TSequenceVValue, typename TScoringScheme,
typename TAlgorithm, typename TTracebackConfig, typename TExecPolicy>
inline typename TraceBitMap_<TScoreValue>::Type
_computeScore(DPCell_<TScoreValue, AffineGaps> & current,
DPCell_<TScoreValue, AffineGaps> & previousDiagonal,
DPCell_<TScoreValue, AffineGaps> const & previousHorizontal,
DPCell_<TScoreValue, AffineGaps> & previousVertical,
TSequenceHValue const & seqHVal,
TSequenceVValue const & seqVVal,
TScoringScheme const & scoringScheme,
RecursionDirectionHorizontal const &,
DPProfile_<TAlgorithm, AffineGaps, TTracebackConfig, TExecPolicy> const &)
{
// Cache previous diagonal value.
_scoreOfCell(previousDiagonal) = _scoreOfCell(previousHorizontal);
// Compute horizontal direction.
auto traceDir = _maxScore(_horizontalScoreOfCell(current),
_horizontalScoreOfCell(previousHorizontal) +
scoreGapExtendHorizontal(scoringScheme, seqHVal, seqVVal),
_scoreOfCell(previousHorizontal) +
scoreGapOpenHorizontal(scoringScheme, seqHVal, seqVVal),
TraceBitMap_<TScoreValue>::HORIZONTAL,
TraceBitMap_<TScoreValue>::HORIZONTAL_OPEN,
TTracebackConfig()) | TraceBitMap_<TScoreValue>::MAX_FROM_HORIZONTAL_MATRIX;
// Ignore vertical direction.
_verticalScoreOfCell(previousVertical) = DPCellDefaultInfinity<DPCell_<TScoreValue, AffineGaps> >::VALUE;
_scoreOfCell(current) = _horizontalScoreOfCell(current);
if (IsLocalAlignment_<TAlgorithm>::VALUE)
{
traceDir = _maxScore(_scoreOfCell(current),
TraceBitMap_<TScoreValue>::NONE,
_scoreOfCell(current),
TraceBitMap_<TScoreValue>::NONE,
traceDir,
TTracebackConfig{});
}
_scoreOfCell(previousVertical) = _scoreOfCell(current);
return traceDir;
}
// ----------------------------------------------------------------------------
// Function _computeScore [RecursionVerticalDirection]
// ----------------------------------------------------------------------------
template <typename TScoreValue,
typename TSequenceHValue, typename TSequenceVValue, typename TScoringScheme,
typename TAlgorithm, typename TTracebackConfig, typename TExecPolicy>
inline typename TraceBitMap_<TScoreValue>::Type
_computeScore(DPCell_<TScoreValue, AffineGaps> & current,
DPCell_<TScoreValue, AffineGaps> const & /*previousDiagonal*/,
DPCell_<TScoreValue, AffineGaps> const & /*previousHorizontal*/,
DPCell_<TScoreValue, AffineGaps> & previousVertical,
TSequenceHValue const & seqHVal,
TSequenceVValue const & seqVVal,
TScoringScheme const & scoringScheme,
RecursionDirectionVertical const &,
DPProfile_<TAlgorithm, AffineGaps, TTracebackConfig, TExecPolicy> const &)
{
// Compute vertical direction.
auto traceDir = _maxScore(_verticalScoreOfCell(previousVertical),
_verticalScoreOfCell(previousVertical) +
scoreGapExtendVertical(scoringScheme, seqHVal, seqVVal),
_scoreOfCell(previousVertical) +
scoreGapOpenVertical(scoringScheme, seqHVal, seqVVal),
TraceBitMap_<TScoreValue>::VERTICAL,
TraceBitMap_<TScoreValue>::VERTICAL_OPEN,
TTracebackConfig()) | TraceBitMap_<TScoreValue>::MAX_FROM_VERTICAL_MATRIX;
// Ignore horizontal direction.
_horizontalScoreOfCell(current) = DPCellDefaultInfinity<DPCell_<TScoreValue, AffineGaps> >::VALUE;
_scoreOfCell(current) = _verticalScoreOfCell(previousVertical);
if (IsLocalAlignment_<TAlgorithm>::VALUE)
{
traceDir = _maxScore(_scoreOfCell(current),
TraceBitMap_<TScoreValue>::NONE,
_scoreOfCell(current),
TraceBitMap_<TScoreValue>::NONE,
traceDir,
TTracebackConfig{});
}
_scoreOfCell(previousVertical) = _scoreOfCell(current);
return traceDir;
}
} // namespace seqan
#endif // #ifndef SEQAN_INCLUDE_SEQAN_ALIGN_DP_FORMULA_AFFINE_H_
