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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>
// ==========================================================================
// Defines the recursion formula for the dp-alignment algorithms.
// ==========================================================================
// TODO(holtgrew): Documentation in this header necessary or internal only?
#ifndef SEQAN_INCLUDE_SEQAN_ALIGN_DP_FORMULA_H_
#define SEQAN_INCLUDE_SEQAN_ALIGN_DP_FORMULA_H_
namespace seqan {
// ============================================================================
// 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
// ============================================================================
// ============================================================================
// Functions
// ============================================================================
// ----------------------------------------------------------------------------
// Function _computeScore
// ----------------------------------------------------------------------------
template <typename TScoreValue, typename TGapCosts, typename TSequenceHValue, typename TSequenceVValue,
typename TScoringScheme, typename TRecursionDirection, typename TDPProfile>
inline SEQAN_FUNC_ENABLE_IF(Not<Is<SimdVectorConcept<TScoreValue> > >, typename TraceBitMap_<TScoreValue>::Type)
_computeScore(DPCell_<TScoreValue, TGapCosts> & activeCell,
DPCell_<TScoreValue, TGapCosts> const & previousDiagonal,
DPCell_<TScoreValue, TGapCosts> const & previousHorizontal,
DPCell_<TScoreValue, TGapCosts> const & previousVertical,
TSequenceHValue const & seqHVal,
TSequenceVValue const & seqVVal,
TScoringScheme const & scoringScheme,
TRecursionDirection const & recDir,
TDPProfile const & dpProfile)
{
typedef typename TraceBitMap_<TScoreValue>::Type TTraceValue;
TTraceValue traceDir = _doComputeScore(activeCell, previousDiagonal, previousHorizontal, previousVertical, seqHVal,
seqVVal, scoringScheme, recDir, dpProfile);
if (IsLocalAlignment_<TDPProfile>::VALUE)
if (activeCell._score <= 0)
{
_setScoreOfCell(activeCell, static_cast<TScoreValue>(0));
_setHorizontalScoreOfCell(activeCell, static_cast<TScoreValue>(0));
_setVerticalScoreOfCell(activeCell, static_cast<TScoreValue>(0));
return TraceBitMap_<TScoreValue>::NONE;
}
return traceDir;
}
template <typename TScoreValue, typename TGapCosts, typename TSequenceHValue, typename TSequenceVValue,
typename TScoringScheme, typename TRecursionDirection, typename TDPProfile>
inline SEQAN_FUNC_ENABLE_IF(Is<SimdVectorConcept<TScoreValue> >, typename TraceBitMap_<TScoreValue>::Type)
_computeScore(DPCell_<TScoreValue, TGapCosts> & activeCell,
DPCell_<TScoreValue, TGapCosts> const & previousDiagonal,
DPCell_<TScoreValue, TGapCosts> const & previousHorizontal,
DPCell_<TScoreValue, TGapCosts> const & previousVertical,
TSequenceHValue const & seqHVal,
TSequenceVValue const & seqVVal,
TScoringScheme const & scoringScheme,
TRecursionDirection const & recDir,
TDPProfile const & dpProfile)
{
typedef typename TraceBitMap_<TScoreValue>::Type TTraceValue;
TTraceValue traceDir = _doComputeScore(activeCell, previousDiagonal, previousHorizontal, previousVertical, seqHVal,
seqVVal, scoringScheme, recDir, dpProfile);
if (IsLocalAlignment_<TDPProfile>::VALUE)
{
TScoreValue cmp = cmpGt(createVector<TScoreValue>(1), activeCell._score);
_setScoreOfCell(activeCell, TraceBitMap_<TScoreValue>::NONE, cmp);
_setHorizontalScoreOfCell(activeCell, TraceBitMap_<TScoreValue>::NONE, cmp);
_setVerticalScoreOfCell(activeCell, TraceBitMap_<TScoreValue>::NONE, cmp);
return blend(traceDir, TraceBitMap_<TScoreValue>::NONE, cmp);
}
return traceDir;
}
// ----------------------------------------------------------------------------
// Function _doComputeScore [RecursionDirectionDiagonal]
// ----------------------------------------------------------------------------
template <typename TScoreValue, typename TGapCosts, typename TSequenceHValue, typename TSequenceVValue, typename TScoringScheme,
typename TDPProfile>
inline typename TraceBitMap_<TScoreValue>::Type
_doComputeScore(DPCell_<TScoreValue, TGapCosts> & activeCell,
DPCell_<TScoreValue, TGapCosts> const & previousDiagonal,
DPCell_<TScoreValue, TGapCosts> const & /*previousHorizontal*/,
DPCell_<TScoreValue, TGapCosts> const & /*previousVertical*/,
TSequenceHValue const & seqHVal,
TSequenceVValue const & seqVVal,
TScoringScheme const & scoringScheme,
RecursionDirectionDiagonal const &,
TDPProfile const &)
{
activeCell._score = _scoreOfCell(previousDiagonal) + score(scoringScheme, seqHVal, seqVVal);
setGapExtension(activeCell, False(), False(), createVector<TScoreValue>(-1));
if (!IsTracebackEnabled_<TDPProfile>::VALUE)
return TraceBitMap_<TScoreValue>::NONE;
return TraceBitMap_<TScoreValue>::DIAGONAL;
}
// ----------------------------------------------------------------------------
// Function _doComputeScore [RecursionDirectionZero]
// ----------------------------------------------------------------------------
template <typename TScoreValue, typename TGapCosts, typename TSequenceHValue, typename TSequenceVValue, typename TScoringScheme,
typename TAlgoTag, typename TTraceFlag>
inline typename TraceBitMap_<TScoreValue>::Type
_doComputeScore(DPCell_<TScoreValue, TGapCosts> & activeCell,
DPCell_<TScoreValue, TGapCosts> const & /*previousDiagonal*/,
DPCell_<TScoreValue, TGapCosts> const & /*previousHorizontal*/,
DPCell_<TScoreValue, TGapCosts> const & /*previousVertical*/,
TSequenceHValue const & /*seqHVal*/,
TSequenceVValue const & /*seqVVal*/,
TScoringScheme const & /*scoringScheme*/,
RecursionDirectionZero const &,
DPProfile_<TAlgoTag, TGapCosts, TTraceFlag> const &)
{
_scoreOfCell(activeCell) = createVector<TScoreValue>(0);
return TraceBitMap_<TScoreValue>::NONE;
}
} // namespace seqan
#endif // #ifndef SEQAN_INCLUDE_SEQAN_ALIGN_DP_FORMULA_H_
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