NVBIO: nvbio::aln::priv::banded::SmithWatermanSubmatrixContext< BAND_LEN, TYPE, CHECKPOINTS, checkpoint_type, submatrix_type > Struct Template Reference

Detailed description

template< uint32 BAND_LEN, AlignmentType TYPE, uint32 CHECKPOINTS, typename checkpoint_type, typename submatrix_type>
struct nvbio::aln::priv::banded::SmithWatermanSubmatrixContext< BAND_LEN, TYPE, CHECKPOINTS, checkpoint_type, submatrix_type >

A helper scoring context class, instantiated to configure sw_alignment_score_dispatch to keep track of the direction vectors of a DP submatrix between given checkpoints

Definition at line 231 of file sw_banded_inl.h.

#include <sw_banded_inl.h>

Public Methods
NVBIO_FORCEINLINE NVBIO_HOST_DEVICE	SmithWatermanSubmatrixContext (const checkpoint_type checkpoints, const uint32 checkpoint_id, submatrix_type submatrix)

template<typename band_type , typename scoring_type , typename score_type >
NVBIO_FORCEINLINE NVBIO_HOST_DEVICE void	init (const uint32 i, band_type &band, const scoring_type &scoring, const score_type infimum)

template<typename band_type >
NVBIO_FORCEINLINE NVBIO_HOST_DEVICE void	previous_row (const uint32 i, const band_type &band)

template<typename band_type >
NVBIO_FORCEINLINE NVBIO_HOST_DEVICE void	last_row (const uint32 i, const band_type &band)

template<typename score_type >
NVBIO_FORCEINLINE NVBIO_HOST_DEVICE void	new_cell (const uint32 i, const uint32 j, const score_type score, const DirectionVector dir)

Public Members
checkpoint_type	m_checkpoints

uint32	m_checkpoint_id

submatrix_type	m_submatrix

Constructor & Destructor Documentation

template<uint32 BAND_LEN, AlignmentType TYPE, uint32 CHECKPOINTS, typename checkpoint_type, typename submatrix_type>

NVBIO_FORCEINLINE NVBIO_HOST_DEVICE nvbio::aln::priv::banded::SmithWatermanSubmatrixContext< BAND_LEN, TYPE, CHECKPOINTS, checkpoint_type, submatrix_type >::SmithWatermanSubmatrixContext	(	const checkpoint_type	checkpoints,
		const uint32	checkpoint_id,
		submatrix_type	submatrix
	)

inline

Definition at line 234 of file sw_banded_inl.h.

Member Function Documentation

template<uint32 BAND_LEN, AlignmentType TYPE, uint32 CHECKPOINTS, typename checkpoint_type, typename submatrix_type>

template<typename band_type , typename scoring_type , typename score_type >

NVBIO_FORCEINLINE NVBIO_HOST_DEVICE void nvbio::aln::priv::banded::SmithWatermanSubmatrixContext< BAND_LEN, TYPE, CHECKPOINTS, checkpoint_type, submatrix_type >::init	(	const uint32	i,
		band_type &	band,
		const scoring_type &	scoring,
		const score_type	infimum
	)

inline

Definition at line 244 of file sw_banded_inl.h.

template<uint32 BAND_LEN, AlignmentType TYPE, uint32 CHECKPOINTS, typename checkpoint_type, typename submatrix_type>

template<typename band_type >

NVBIO_FORCEINLINE NVBIO_HOST_DEVICE void nvbio::aln::priv::banded::SmithWatermanSubmatrixContext< BAND_LEN, TYPE, CHECKPOINTS, checkpoint_type, submatrix_type >::last_row	(	const uint32	i,
		const band_type &	band
	)

inline

Definition at line 264 of file sw_banded_inl.h.

template<uint32 BAND_LEN, AlignmentType TYPE, uint32 CHECKPOINTS, typename checkpoint_type, typename submatrix_type>

template<typename score_type >

NVBIO_FORCEINLINE NVBIO_HOST_DEVICE void nvbio::aln::priv::banded::SmithWatermanSubmatrixContext< BAND_LEN, TYPE, CHECKPOINTS, checkpoint_type, submatrix_type >::new_cell	(	const uint32	i,
		const uint32	j,
		const score_type	score,
		const DirectionVector	dir
	)

inline

Definition at line 270 of file sw_banded_inl.h.

template<uint32 BAND_LEN, AlignmentType TYPE, uint32 CHECKPOINTS, typename checkpoint_type, typename submatrix_type>

template<typename band_type >

NVBIO_FORCEINLINE NVBIO_HOST_DEVICE void nvbio::aln::priv::banded::SmithWatermanSubmatrixContext< BAND_LEN, TYPE, CHECKPOINTS, checkpoint_type, submatrix_type >::previous_row	(	const uint32	i,
		const band_type &	band
	)

inline

Definition at line 258 of file sw_banded_inl.h.

Member Data Documentation

template<uint32 BAND_LEN, AlignmentType TYPE, uint32 CHECKPOINTS, typename checkpoint_type, typename submatrix_type>

uint32 nvbio::aln::priv::banded::SmithWatermanSubmatrixContext< BAND_LEN, TYPE, CHECKPOINTS, checkpoint_type, submatrix_type >::m_checkpoint_id

Definition at line 282 of file sw_banded_inl.h.

template<uint32 BAND_LEN, AlignmentType TYPE, uint32 CHECKPOINTS, typename checkpoint_type, typename submatrix_type>

checkpoint_type nvbio::aln::priv::banded::SmithWatermanSubmatrixContext< BAND_LEN, TYPE, CHECKPOINTS, checkpoint_type, submatrix_type >::m_checkpoints

Definition at line 281 of file sw_banded_inl.h.

template<uint32 BAND_LEN, AlignmentType TYPE, uint32 CHECKPOINTS, typename checkpoint_type, typename submatrix_type>

submatrix_type nvbio::aln::priv::banded::SmithWatermanSubmatrixContext< BAND_LEN, TYPE, CHECKPOINTS, checkpoint_type, submatrix_type >::m_submatrix

Definition at line 283 of file sw_banded_inl.h.

The documentation for this struct was generated from the following file:

E:/git/nvbio/nvbio/alignment/sw/sw_banded_inl.h