// ==========================================================================
// SeqAn - The Library for Sequence Analysis
// ==========================================================================
// Copyright (c) 2006-2018, Knut Reinert, FU Berlin
// All rights reserved.
//
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// modification, are permitted provided that the following conditions are met:
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// * Redistributions of source code must retain the above copyright
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// ==========================================================================
// Author: Rene Rahn <rene.rahn@fu-berlin.de>
// ==========================================================================
// Defines the methods to compute the score when using linear gap costs.
// ==========================================================================
#ifndef SEQAN_INCLUDE_SEQAN_ALIGN_DP_FORMULA_LINEAR_H_
#define SEQAN_INCLUDE_SEQAN_ALIGN_DP_FORMULA_LINEAR_H_
namespace seqan {
// ============================================================================
// Forwards
// ============================================================================
// ============================================================================
// Tags, Classes, Enums
// ============================================================================
// ============================================================================
// Metafunctions
// ============================================================================
// ============================================================================
// Functions
// ============================================================================
// ----------------------------------------------------------------------------
// Function _computeScore [RecursionDirectionAll, LinearGaps]
// ----------------------------------------------------------------------------
template <typename TScoreValue, typename TSequenceHValue, typename TSequenceVValue, typename TScoringScheme,
typename TAlgorithm, typename TTracebackConfig, typename TExecPolicy>
inline typename TraceBitMap_<TScoreValue>::Type
_computeScore(DPCell_<TScoreValue, LinearGaps> & current,
DPCell_<TScoreValue, LinearGaps> & previousDiagonal,
DPCell_<TScoreValue, LinearGaps> const & previousHorizontal,
DPCell_<TScoreValue, LinearGaps> & previousVertical,
TSequenceHValue const & seqHVal,
TSequenceVValue const & seqVVal,
TScoringScheme const & scoringScheme,
RecursionDirectionAll const &,
DPProfile_<TAlgorithm, LinearGaps, TTracebackConfig, TExecPolicy> const &)
{
// Cache next diagonal.
auto intermediate = static_cast<TScoreValue>(_scoreOfCell(previousDiagonal) + score(scoringScheme, seqHVal, seqVVal));
previousDiagonal = _scoreOfCell(previousHorizontal);
auto tv = _maxScore(_scoreOfCell(current),
_scoreOfCell(previousVertical)+
scoreGapExtendVertical(scoringScheme, seqHVal, seqVVal),
_scoreOfCell(previousHorizontal) +
scoreGapExtendHorizontal(scoringScheme, seqHVal, seqVVal),
TraceBitMap_<TScoreValue>::VERTICAL | TraceBitMap_<TScoreValue>::MAX_FROM_VERTICAL_MATRIX,
TraceBitMap_<TScoreValue>::HORIZONTAL | TraceBitMap_<TScoreValue>::MAX_FROM_HORIZONTAL_MATRIX,
TTracebackConfig{});
// Compute the intermediate value.
tv = _maxScore(_scoreOfCell(current),
intermediate,
_scoreOfCell(current),
TraceBitMap_<TScoreValue>::DIAGONAL,
tv,
TTracebackConfig());
if (IsLocalAlignment_<TAlgorithm>::VALUE)
{
tv = _maxScore(_scoreOfCell(current),
TraceBitMap_<TScoreValue>::NONE,
_scoreOfCell(current),
TraceBitMap_<TScoreValue>::NONE,
tv,
TTracebackConfig{});
}
previousVertical = current;
return tv;
}
// ----------------------------------------------------------------------------
// Function _computeScore [RecursionDirectionUpperDiagonal, LinearGaps]
// ----------------------------------------------------------------------------
template <typename TScoreValue, typename TSequenceHValue, typename TSequenceVValue, typename TScoringScheme,
typename TAlgorithm, typename TTracebackConfig, typename TExecPolicy>
inline typename TraceBitMap_<TScoreValue>::Type
_computeScore(DPCell_<TScoreValue, LinearGaps> & current,
DPCell_<TScoreValue, LinearGaps> & previousDiagonal,
DPCell_<TScoreValue, LinearGaps> const & previousHorizontal,
DPCell_<TScoreValue, LinearGaps> & previousVertical,
TSequenceHValue const & seqHVal,
TSequenceVValue const & seqVVal,
TScoringScheme const & scoringScheme,
RecursionDirectionUpperDiagonal const &,
DPProfile_<TAlgorithm, LinearGaps, TTracebackConfig, TExecPolicy> const &)
{
// Precalculate diagonal direction.
auto intermediate = static_cast<TScoreValue>(_scoreOfCell(previousDiagonal) + score(scoringScheme, seqHVal, seqVVal));
// Cache next diagonal value.
previousDiagonal = _scoreOfCell(previousHorizontal);
auto tv = _maxScore(_scoreOfCell(current),
intermediate,
_scoreOfCell(previousHorizontal) + scoreGapExtendHorizontal(scoringScheme, seqHVal, seqVVal),
TraceBitMap_<TScoreValue>::DIAGONAL,
TraceBitMap_<TScoreValue>::HORIZONTAL | 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{});
}
previousVertical = current;
return tv;
}
// ----------------------------------------------------------------------------
// Function _computeScore [RecursionDirectionLowerDiagonal, LinearGaps]
// ----------------------------------------------------------------------------
template <typename TScoreValue, typename TSequenceHValue, typename TSequenceVValue, typename TScoringScheme,
typename TAlgorithm, typename TTracebackConfig, typename TExecPolicy>
inline typename TraceBitMap_<TScoreValue>::Type
_computeScore(DPCell_<TScoreValue, LinearGaps> & current,
DPCell_<TScoreValue, LinearGaps> const & previousDiagonal,
DPCell_<TScoreValue, LinearGaps> const & /*previousHorizontal*/,
DPCell_<TScoreValue, LinearGaps> const & previousVertical,
TSequenceHValue const & seqHVal,
TSequenceVValue const & seqVVal,
TScoringScheme const & scoringScheme,
RecursionDirectionLowerDiagonal const &,
DPProfile_<TAlgorithm, LinearGaps, TTracebackConfig, TExecPolicy> const &)
{
auto tv = _maxScore(_scoreOfCell(current),
static_cast<TScoreValue>(_scoreOfCell(previousDiagonal) +
score(scoringScheme, seqHVal, seqVVal)),
static_cast<TScoreValue>(_scoreOfCell(previousVertical) +
scoreGapExtendVertical(scoringScheme, seqHVal, seqVVal)),
TraceBitMap_<TScoreValue>::DIAGONAL,
TraceBitMap_<TScoreValue>::VERTICAL | 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 [RecursionDirectionHorizontal]
// ----------------------------------------------------------------------------
template <typename TScoreValue, typename TSequenceHValue, typename TSequenceVValue, typename TScoringScheme,
typename TAlgorithm, typename TTracebackConfig, typename TExecPolicy>
inline typename TraceBitMap_<TScoreValue>::Type
_computeScore(DPCell_<TScoreValue, LinearGaps> & activeCell,
DPCell_<TScoreValue, LinearGaps> & previousDiagonal,
DPCell_<TScoreValue, LinearGaps> const & previousHorizontal,
DPCell_<TScoreValue, LinearGaps> & previousVertical,
TSequenceHValue const & seqHVal,
TSequenceVValue const & seqVVal,
TScoringScheme const & scoringScheme,
RecursionDirectionHorizontal const &,
DPProfile_<TAlgorithm, LinearGaps, TTracebackConfig, TExecPolicy> const &)
{
// Cache previous diagonal.
previousDiagonal = previousHorizontal;
// Compute current value.
_scoreOfCell(activeCell) = _scoreOfCell(previousHorizontal) +
scoreGapExtendHorizontal(scoringScheme, seqHVal, seqVVal);
auto tv = TraceBitMap_<TScoreValue>::HORIZONTAL | TraceBitMap_<TScoreValue>::MAX_FROM_HORIZONTAL_MATRIX;
if (IsLocalAlignment_<TAlgorithm>::VALUE)
{
tv = _maxScore(_scoreOfCell(activeCell),
TraceBitMap_<TScoreValue>::NONE,
_scoreOfCell(activeCell),
TraceBitMap_<TScoreValue>::NONE,
tv,
TTracebackConfig{});
}
// Cache next vertical.
previousVertical = activeCell;
return tv;
}
// ----------------------------------------------------------------------------
// Function _computeScore [RecursionDirectionVertical]
// ----------------------------------------------------------------------------
template <typename TScoreValue, typename TSequenceHValue, typename TSequenceVValue, typename TScoringScheme,
typename TAlgorithm, typename TTracebackConfig, typename TExecPolicy>
inline typename TraceBitMap_<TScoreValue>::Type
_computeScore(DPCell_<TScoreValue, LinearGaps> & current,
DPCell_<TScoreValue, LinearGaps> const & /*previousDiagonal*/,
DPCell_<TScoreValue, LinearGaps> const & /*previousHorizontal*/,
DPCell_<TScoreValue, LinearGaps> & previousVertical,
TSequenceHValue const & seqHVal,
TSequenceVValue const & seqVVal,
TScoringScheme const & scoringScheme,
RecursionDirectionVertical const &,
DPProfile_<TAlgorithm, LinearGaps, TTracebackConfig, TExecPolicy> const &)
{
_scoreOfCell(current) = _scoreOfCell(previousVertical) + scoreGapExtendVertical(scoringScheme, seqHVal, seqVVal);
auto tv = TraceBitMap_<TScoreValue>::VERTICAL | TraceBitMap_<TScoreValue>::MAX_FROM_VERTICAL_MATRIX;
if (IsLocalAlignment_<TAlgorithm>::VALUE)
{
tv = _maxScore(_scoreOfCell(current),
TraceBitMap_<TScoreValue>::NONE,
_scoreOfCell(current),
TraceBitMap_<TScoreValue>::NONE,
tv,
TTracebackConfig{});
}
// Cache previous vertical.
previousVertical = current;
return tv;
}
} // namespace seqan
#endif // #ifndef SEQAN_INCLUDE_SEQAN_ALIGN_DP_FORMULA_LINEAR_H_
