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// ==========================================================================
// 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
// 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: Manuel Holtgrewe <manuel.holtgrewe@fu-berlin.de>
// ==========================================================================
// DPScout_ specialization for the split alignment implementation.
// ==========================================================================
#ifndef SEQAN_INCLUDE_SEQAN_ALIGN_SPLIT_DP_SCOUT_SPLIT_H_
#define SEQAN_INCLUDE_SEQAN_ALIGN_SPLIT_DP_SCOUT_SPLIT_H_
namespace seqan {
// ============================================================================
// Forwards
// ============================================================================
// ============================================================================
// Tags, Classes, Enums
// ============================================================================
// ----------------------------------------------------------------------------
// Tag SplitAlignmentScout.
// ----------------------------------------------------------------------------
struct SplitAlignmentScout_;
typedef Tag<SplitAlignmentScout_> SplitAlignmentScout;
// ----------------------------------------------------------------------------
// Class DPScoutState_
// ----------------------------------------------------------------------------
template <>
class DPScoutState_<SplitAlignmentScout>
{
public:
// The best score for each column. Initialized with 0.5*minValue<TScoreVal>().
seqan::String<int> splitScore;
seqan::String<int> splitPos;
DPScoutState_()
{}
};
// ----------------------------------------------------------------------------
// Class DPScout_
// ----------------------------------------------------------------------------
template <typename TDPCell>
class DPScout_<TDPCell, SplitAlignmentScout> : public DPScout_<TDPCell, Default>
{
public:
typedef DPScout_<TDPCell, Default> TParent;
DPScoutState_<SplitAlignmentScout> * state;
DPScout_() : TParent(), state(0)
{}
DPScout_(DPScoutState_<SplitAlignmentScout> & state) : TParent(), state(&state)
{}
};
// ============================================================================
// Metafunctions
// ============================================================================
// ============================================================================
// Functions
// ============================================================================
// ----------------------------------------------------------------------------
// Function _scoutBestScore() [DPScout_]
// ----------------------------------------------------------------------------
template <typename TDPCell, typename TTraceMatrixNavigator, typename TIsLastColumn, typename TIsLastRow>
inline void
_scoutBestScore(DPScout_<TDPCell, SplitAlignmentScout> & dpScout,
TDPCell const & activeCell,
TTraceMatrixNavigator const & navigator,
TIsLastColumn /*isLastColumn*/,
TIsLastRow /*isLastRow*/ )
{
//typedef typename Value<TDPCell>::Type TScoreValue;
// Note that the underlying matrix has the coordinates flipped. We use posH/posV as we would in pairwise alignments
// and thus this is the reverse from the matrix representation.
unsigned posH = coordinate(navigator, +DPMatrixDimension_::HORIZONTAL);
// unsigned posV = coordinate(navigator, +DPMatrixDimension_::VERTICAL);
int & i = dpScout.state->splitScore[posH];
if (i < _scoreOfCell(activeCell))
{
i = _scoreOfCell(activeCell);
dpScout.state->splitPos[posH] = position(navigator);
}
// TODO(rrahn): Do we need the optimal end-point?
// We track only the last row for the best traceback score.
if (TIsLastColumn::VALUE || TIsLastRow::VALUE)
{
typedef DPScout_<TDPCell, SplitAlignmentScout> TDPScout;
typedef typename TDPScout::TParent TParent;
_scoutBestScore(static_cast<TParent &>(dpScout), activeCell, navigator);
}
}
} // namespace seqan
#endif // #ifndef SEQAN_INCLUDE_SEQAN_ALIGN_SPLIT_DP_SCOUT_SPLIT_H_
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