// ==========================================================================
// SeqAn - The Library for Sequence Analysis
// ==========================================================================
// Copyright (c) 2006-2018, Knut Reinert, FU Berlin
// All rights reserved.
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// ==========================================================================
// Author: Rene Rahn <rene.rahn@fu-berlin.de>
// ==========================================================================
// The navigator for the full score dp-matrix. We need two iterators over the
// current column and the previous column. We also store the three neighboring
// cells needed for the recursion formula.
// ==========================================================================
#ifndef SEQAN_INCLUDE_SEQAN_ALIGN_DP_MATRIX_NAVIGATOR_SCORE_H_
#define SEQAN_INCLUDE_SEQAN_ALIGN_DP_MATRIX_NAVIGATOR_SCORE_H_
namespace seqan {
// ============================================================================
// Forwards
// ============================================================================
// ============================================================================
// Tags, Classes, Enums
// ============================================================================
// ----------------------------------------------------------------------------
// Class DPMatrixNavigator [FullDPMatrix, ScoreMatrix]
// ----------------------------------------------------------------------------
// The navigator for the score matrix.
//
// This navigator runs on a FullDPMatrix while it navigates column wise.
template <typename TValue, typename THost, typename TNavigationSpec>
class DPMatrixNavigator_<DPMatrix_<TValue, FullDPMatrix, THost>, DPScoreMatrix, TNavigationSpec>
{
public:
typedef DPMatrix_<TValue, FullDPMatrix, THost> TDPMatrix_;
typedef typename Pointer_<TDPMatrix_>::Type TDPMatrixPointer_;
typedef typename Iterator<TDPMatrix_, Standard>::Type TDPMatrixIterator;
template <typename TBandSpec,
std::enable_if_t<std::is_same<TBandSpec, BandOff>::value, int> = 0>
DPMatrixNavigator_(TDPMatrix_ & matrix,
DPBandConfig<TBandSpec> const & /*band*/)
{
_ptrDataContainer = &matrix;
_prevColIteratorOffset = _dataFactors(matrix)[DPMatrixDimension_::HORIZONTAL];
_activeColIterator = begin(matrix, Standard());
_prevColIterator = _activeColIterator - _prevColIteratorOffset;
_laneLeap = 1;
*_activeColIterator = TValue();
}
template <typename TBandSpec,
std::enable_if_t<!std::is_same<TBandSpec, BandOff>::value, int> = 0>
DPMatrixNavigator_(TDPMatrix_ & matrix,
DPBandConfig<TBandSpec> const & band)
{
using TMatrixSize = typename Size<TDPMatrix_>::Type;
using TSignedSize = std::make_signed_t<TMatrixSize>;
_ptrDataContainer = &matrix;
_prevColIteratorOffset = _dataFactors(matrix)[DPMatrixDimension_::HORIZONTAL];
// Band begins within the first row.
if (lowerDiagonal(band) >= 0)
{
_laneLeap = _min(length(matrix, DPMatrixDimension_::VERTICAL), bandSize(band));
_activeColIterator = begin(matrix, Standard()) + _dataLengths(matrix)[DPMatrixDimension_::VERTICAL] - 1;
}
else if (upperDiagonal(band) <= 0) // Band begins within the first column.
{
_laneLeap = 1;
_activeColIterator = begin(matrix, Standard());
}
else // Band intersects with the point of origin.
{
TMatrixSize lengthVertical = length(matrix, DPMatrixDimension_::VERTICAL);
int lastPos = _max(-static_cast<TSignedSize>(lengthVertical - 1), lowerDiagonal(band));
_laneLeap = lengthVertical + lastPos;
_activeColIterator = begin(matrix, Standard()) + _laneLeap - 1;
}
// Set previous iterator to same position, one column left.
_prevColIterator = _activeColIterator - _prevColIteratorOffset;
*_activeColIterator = TValue();
}
TDPMatrixPointer_ _ptrDataContainer{nullptr}; // Pointer to the matrix this navigator is working on.
int _laneLeap{0}; // Stores the jump to the next column
size_t _prevColIteratorOffset{0}; // Offset to reset the previous column iterator when going to the next cell.
TDPMatrixIterator _activeColIterator{}; // The active column iterator.
TDPMatrixIterator _prevColIterator{}; // The previous column iterator.
};
// ============================================================================
// Metafunctions
// ============================================================================
// ============================================================================
// Functions
// ============================================================================
// ----------------------------------------------------------------------------
// Function _goNextCell [banded, FirstCell]
// ----------------------------------------------------------------------------
// Needed to avoid ambigious overload.
template <typename TValue, typename TDPMatrixSpec, typename THost>
inline void
_goNextCell(DPMatrixNavigator_<DPMatrix_<TValue, TDPMatrixSpec, THost>, DPScoreMatrix, NavigateColumnWiseBanded> & /*dpNavigator*/,
MetaColumnDescriptor<DPInitialColumn, PartialColumnTop> const &,
FirstCell const &)
{
// no-op
}
// Needed to avoid ambigious overload.
template <typename TValue, typename TDPMatrixSpec, typename THost>
inline void
_goNextCell(DPMatrixNavigator_<DPMatrix_<TValue, TDPMatrixSpec, THost>, DPScoreMatrix, NavigateColumnWiseBanded> & /*dpNavigator*/,
MetaColumnDescriptor<DPInitialColumn, FullColumn> const &,
FirstCell const &)
{
// no-op
}
// specialized for initialization column and all other column locations.
template <typename TValue, typename TDPMatrixSpec, typename THost,
typename TColumnLocation>
inline void
_goNextCell(DPMatrixNavigator_<DPMatrix_<TValue, TDPMatrixSpec, THost>, DPScoreMatrix, NavigateColumnWiseBanded> & /*dpNavigator*/,
MetaColumnDescriptor<DPInitialColumn, TColumnLocation> const &,
FirstCell const &)
{
// no-op
}
// specialized for all other column types located at the top.
template <typename TValue, typename TDPMatrixSpec, typename THost,
typename TColumnType>
inline void
_goNextCell(DPMatrixNavigator_<DPMatrix_<TValue, TDPMatrixSpec, THost>, DPScoreMatrix, NavigateColumnWiseBanded> & dpNavigator,
MetaColumnDescriptor<TColumnType, PartialColumnTop> const &,
FirstCell const &)
{
--dpNavigator._laneLeap;
dpNavigator._activeColIterator += dpNavigator._laneLeap;
dpNavigator._prevColIterator = dpNavigator._activeColIterator - dpNavigator._prevColIteratorOffset + 1;
}
template <typename TValue, typename TDPMatrixSpec, typename THost,
typename TColumnType>
inline void
_goNextCell(DPMatrixNavigator_<DPMatrix_<TValue, TDPMatrixSpec, THost>, DPScoreMatrix, NavigateColumnWiseBanded> & dpNavigator,
MetaColumnDescriptor<TColumnType, FullColumn> const &,
FirstCell const &)
{
dpNavigator._activeColIterator += dpNavigator._laneLeap;
dpNavigator._prevColIterator = dpNavigator._activeColIterator - dpNavigator._prevColIteratorOffset;
}
// version for all other column types and locations.
template <typename TValue, typename TDPMatrixSpec, typename THost,
typename TColumnType, typename TColumnLocation>
inline void
_goNextCell(DPMatrixNavigator_<DPMatrix_<TValue, TDPMatrixSpec, THost>, DPScoreMatrix, NavigateColumnWiseBanded> & dpNavigator,
MetaColumnDescriptor<TColumnType, TColumnLocation> const &,
FirstCell const &)
{
dpNavigator._activeColIterator += dpNavigator._laneLeap;
dpNavigator._prevColIterator = dpNavigator._activeColIterator - dpNavigator._prevColIteratorOffset + 1;
}
// ----------------------------------------------------------------------------
// Function _goNextCell [unbanded, FirstCell]
// ----------------------------------------------------------------------------
// specialized for initalization column.
template <typename TValue, typename THost>
inline void
_goNextCell(DPMatrixNavigator_<DPMatrix_<TValue, FullDPMatrix, THost>, DPScoreMatrix, NavigateColumnWise> & /*dpNavigator*/,
MetaColumnDescriptor<DPInitialColumn, FullColumn> const &,
FirstCell const &)
{
// no-op
}
// all other column types.
template <typename TValue, typename THost,
typename TColumnType>
inline void
_goNextCell(DPMatrixNavigator_<DPMatrix_<TValue, FullDPMatrix, THost>, DPScoreMatrix, NavigateColumnWise> & dpNavigator,
MetaColumnDescriptor<TColumnType, FullColumn> const &,
FirstCell const &)
{
// Set to begin of column.
dpNavigator._activeColIterator += dpNavigator._laneLeap;
dpNavigator._prevColIterator = dpNavigator._activeColIterator - dpNavigator._prevColIteratorOffset;
}
// ----------------------------------------------------------------------------
// Function _goNextCell [banded, InnerCell]
// ----------------------------------------------------------------------------
// specilized for the initialization column and all column locations.
template <typename TValue, typename TDPMatrixSpec, typename THost,
typename TColumnLocation>
inline void
_goNextCell(DPMatrixNavigator_<DPMatrix_<TValue, TDPMatrixSpec, THost>, DPScoreMatrix, NavigateColumnWiseBanded> & dpNavigator,
MetaColumnDescriptor<DPInitialColumn, TColumnLocation> const &,
InnerCell const &)
{
++dpNavigator._activeColIterator;
}
// specialized for the standard band processing.
template <typename TValue, typename TDPMatrixSpec, typename THost,
typename TColumnType, typename TColumnLocation>
inline void
_goNextCell(DPMatrixNavigator_<DPMatrix_<TValue, TDPMatrixSpec, THost>, DPScoreMatrix, NavigateColumnWiseBanded> & dpNavigator,
MetaColumnDescriptor<TColumnType, TColumnLocation> const &,
InnerCell const &)
{
++dpNavigator._activeColIterator;
++dpNavigator._prevColIterator;
}
// ----------------------------------------------------------------------------
// Function _goNextCell [unbanded, InnerCell]
// ----------------------------------------------------------------------------
// specialized for the initialization column.
template <typename TValue, typename THost>
inline void
_goNextCell(DPMatrixNavigator_<DPMatrix_<TValue, FullDPMatrix, THost>, DPScoreMatrix, NavigateColumnWise> & dpNavigator,
MetaColumnDescriptor<DPInitialColumn, FullColumn> const &,
InnerCell const &)
{
++dpNavigator._activeColIterator;
}
// version for the all other column types.
template <typename TValue, typename THost,
typename TColumnType>
inline void
_goNextCell(DPMatrixNavigator_<DPMatrix_<TValue, FullDPMatrix, THost>, DPScoreMatrix, NavigateColumnWise> & dpNavigator,
MetaColumnDescriptor<TColumnType, FullColumn> const &,
InnerCell const &)
{
++dpNavigator._activeColIterator;
++dpNavigator._prevColIterator;
}
// ----------------------------------------------------------------------------
// Function _goNextCell [banded, LastCell]
// ----------------------------------------------------------------------------
// specilaized for initialization column and bottom column.
template <typename TValue, typename TDPMatrixSpec, typename THost>
inline void
_goNextCell(DPMatrixNavigator_<DPMatrix_<TValue, TDPMatrixSpec, THost>, DPScoreMatrix, NavigateColumnWiseBanded> & dpNavigator,
MetaColumnDescriptor<DPInitialColumn, PartialColumnBottom> const &,
LastCell const &)
{
++dpNavigator._activeColIterator;
}
// specilaized for initialization column and all other column locations.
template <typename TValue, typename TDPMatrixSpec, typename THost,
typename TColumnLocation>
inline void
_goNextCell(DPMatrixNavigator_<DPMatrix_<TValue, TDPMatrixSpec, THost>, DPScoreMatrix, NavigateColumnWiseBanded> & dpNavigator,
MetaColumnDescriptor<DPInitialColumn, TColumnLocation> const &,
LastCell const &)
{
++dpNavigator._activeColIterator;
}
// specialized for all column types and bottom column.
template <typename TValue, typename TDPMatrixSpec, typename THost,
typename TColumnType>
inline void
_goNextCell(DPMatrixNavigator_<DPMatrix_<TValue, TDPMatrixSpec, THost>, DPScoreMatrix, NavigateColumnWiseBanded> & dpNavigator,
MetaColumnDescriptor<TColumnType, PartialColumnBottom> const &,
LastCell const &)
{
++dpNavigator._activeColIterator;
++dpNavigator._prevColIterator;
++dpNavigator._laneLeap;
}
// generic case for all other column types and column locations.
template <typename TValue, typename TDPMatrixSpec, typename THost,
typename TColumnType, typename TColumnLocation>
inline void
_goNextCell(DPMatrixNavigator_<DPMatrix_<TValue, TDPMatrixSpec, THost>, DPScoreMatrix, NavigateColumnWiseBanded> & dpNavigator,
MetaColumnDescriptor<TColumnType, TColumnLocation> const &,
LastCell const &)
{
++dpNavigator._activeColIterator;
++dpNavigator._prevColIterator;
}
// ----------------------------------------------------------------------------
// Function _goNextCell [unbanded, LastCell]
// ----------------------------------------------------------------------------
// specilaized for initialization column.
template <typename TValue, typename THost>
inline void
_goNextCell(DPMatrixNavigator_<DPMatrix_<TValue, FullDPMatrix, THost>, DPScoreMatrix, NavigateColumnWise> & dpNavigator,
MetaColumnDescriptor<DPInitialColumn, FullColumn> const &,
LastCell const &)
{
++dpNavigator._activeColIterator;
}
// version for all other column types.
template <typename TValue, typename THost,
typename TColumnType>
inline void
_goNextCell(DPMatrixNavigator_<DPMatrix_<TValue, FullDPMatrix, THost>, DPScoreMatrix, NavigateColumnWise> & dpNavigator,
MetaColumnDescriptor<TColumnType, FullColumn> const &,
LastCell const &)
{
++dpNavigator._activeColIterator; // go to next cell.
++dpNavigator._prevColIterator; // go to next cell.
}
// ----------------------------------------------------------------------------
// Function _preInitCacheDiagonal()
// ----------------------------------------------------------------------------
template <typename TDPCell,
typename TValue, typename TMatrixSpec, typename THost,
typename TColumnType>
inline void
_preInitCacheDiagonal(TDPCell & cacheDiagonal,
DPMatrixNavigator_<DPMatrix_<TValue, TMatrixSpec, THost>, DPScoreMatrix, NavigateColumnWiseBanded> const & dpNavigator,
MetaColumnDescriptor<TColumnType, PartialColumnMiddle> const & /*tag*/)
{
_scoreOfCell(cacheDiagonal) = _scoreOfCell(*(dpNavigator._prevColIterator - 1));
}
template <typename TDPCell,
typename TValue, typename TMatrixSpec, typename THost,
typename TColumnType>
inline void
_preInitCacheDiagonal(TDPCell & cacheDiagonal,
DPMatrixNavigator_<DPMatrix_<TValue, TMatrixSpec, THost>, DPScoreMatrix, NavigateColumnWiseBanded> const & dpNavigator,
MetaColumnDescriptor<TColumnType, PartialColumnBottom> const & /*tag*/)
{
_scoreOfCell(cacheDiagonal) = _scoreOfCell(*(dpNavigator._prevColIterator - 1));
}
template <typename TDPCell,
typename TValue, typename TMatrixSpec, typename THost, typename TNavigationSpec,
typename TColumnType, typename TColumnLocation>
inline void
_preInitCacheDiagonal(TDPCell & /*cacheDiagonal*/,
DPMatrixNavigator_<DPMatrix_<TValue, TMatrixSpec, THost>, DPScoreMatrix, TNavigationSpec> const & /*dpNavigator*/,
MetaColumnDescriptor<TColumnType, TColumnLocation> const & /*tag*/)
{
// no-op
}
// ----------------------------------------------------------------------------
// Function previousCellHorizontal()
// ----------------------------------------------------------------------------
template <typename TDPMatrix, typename TNavigationSpec>
inline typename Reference<DPMatrixNavigator_<TDPMatrix, DPScoreMatrix, TNavigationSpec> >::Type
previousCellHorizontal(DPMatrixNavigator_<TDPMatrix, DPScoreMatrix, TNavigationSpec> & dpNavigator)
{
return *dpNavigator._prevColIterator;
}
template <typename TDPMatrix, typename TNavigationSpec>
inline typename Reference<DPMatrixNavigator_<TDPMatrix, DPScoreMatrix, TNavigationSpec> const>::Type
previousCellHorizontal(DPMatrixNavigator_<TDPMatrix, DPScoreMatrix, TNavigationSpec> const & dpNavigator)
{
return *dpNavigator._prevColIterator;
}
} // namespace seqan
#endif // #ifndef SEQAN_INCLUDE_SEQAN_ALIGN_DP_MATRIX_NAVIGATOR_SCORE_H_
