nvbio::aln::priv::banded::SmithWatermanScoringContext< BAND_LEN, TYPE > Struct Template Reference

Detailed description

template< uint32 BAND_LEN, AlignmentType TYPE>
struct nvbio::aln::priv::banded::SmithWatermanScoringContext< BAND_LEN, TYPE >

A helper scoring context class, which can be used to adapt the basic sw_alignment_score_dispatch algorithm to various situations, such as: scoring scoring within a window (i.e. saving only the last band within the window) computing checkpoints computing a flow submatrix

Definition at line 65 of file sw_banded_inl.h.

#include <sw_banded_inl.h>

Public Methods
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)

Member Function Documentation

template<uint32 BAND_LEN, AlignmentType TYPE>

template<typename band_type , typename scoring_type , typename score_type >

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

inline

Definition at line 69 of file sw_banded_inl.h.

template<uint32 BAND_LEN, AlignmentType TYPE>

template<typename band_type >

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

inline

Definition at line 86 of file sw_banded_inl.h.

template<uint32 BAND_LEN, AlignmentType TYPE>

template<typename score_type >

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

inline

Definition at line 92 of file sw_banded_inl.h.

template<uint32 BAND_LEN, AlignmentType TYPE>

template<typename band_type >

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

inline

Definition at line 80 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