nvbio::aln::priv::banded::GotohCheckpointContext< BAND_LEN, TYPE, CHECKPOINTS, checkpoint_type > Struct Template Reference

Detailed description

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

A helper scoring context class, instantiated to configure gotoh_alignment_score_dispatch to store checkpoints of the banded DP matrix along the pattern

Definition at line 206 of file gotoh_banded_inl.h.

#include <gotoh_banded_inl.h>

Public Methods
NVBIO_FORCEINLINE NVBIO_HOST_DEVICE	GotohCheckpointContext (checkpoint_type checkpoints)
template<typename H_band_type , typename F_band_type , typename scoring_type , typename score_type >
NVBIO_FORCEINLINE NVBIO_HOST_DEVICE void	init (const uint32 i, H_band_type &H_band, F_band_type &F_band, const scoring_type &scoring, const score_type infimum)
template<typename H_band_type , typename F_band_type >
NVBIO_FORCEINLINE NVBIO_HOST_DEVICE void	previous_row (const uint32 i, const H_band_type &H_band, const F_band_type &F_band)
template<typename H_band_type , typename F_band_type >
NVBIO_FORCEINLINE NVBIO_HOST_DEVICE void	last_row (const uint32 i, const H_band_type &H_band, const F_band_type &F_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, const DirectionVector edir, const DirectionVector fdir)

Public Members
checkpoint_type	m_checkpoints

Constructor & Destructor Documentation

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

NVBIO_FORCEINLINE NVBIO_HOST_DEVICE nvbio::aln::priv::banded::GotohCheckpointContext< BAND_LEN, TYPE, CHECKPOINTS, checkpoint_type >::GotohCheckpointContext ( checkpoint_type  checkpoints)

inline

Definition at line 209 of file gotoh_banded_inl.h.

Member Function Documentation

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

template<typename H_band_type , typename F_band_type , typename scoring_type , typename score_type >

NVBIO_FORCEINLINE NVBIO_HOST_DEVICE void nvbio::aln::priv::banded::GotohCheckpointContext< BAND_LEN, TYPE, CHECKPOINTS, checkpoint_type >::init ( const uint32  i, H_band_type &  H_band, F_band_type &  F_band, const scoring_type &  scoring, const score_type  infimum  )

inline

Definition at line 214 of file gotoh_banded_inl.h.

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

template<typename H_band_type , typename F_band_type >

NVBIO_FORCEINLINE NVBIO_HOST_DEVICE void nvbio::aln::priv::banded::GotohCheckpointContext< BAND_LEN, TYPE, CHECKPOINTS, checkpoint_type >::last_row ( const uint32  i, const H_band_type &  H_band, const F_band_type &  F_band  )

inline

Definition at line 245 of file gotoh_banded_inl.h.

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

template<typename score_type >

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

inline

Definition at line 263 of file gotoh_banded_inl.h.

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

template<typename H_band_type , typename F_band_type >

NVBIO_FORCEINLINE NVBIO_HOST_DEVICE void nvbio::aln::priv::banded::GotohCheckpointContext< BAND_LEN, TYPE, CHECKPOINTS, checkpoint_type >::previous_row ( const uint32  i, const H_band_type &  H_band, const F_band_type &  F_band  )

inline

Definition at line 226 of file gotoh_banded_inl.h.

Member Data Documentation

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

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

Definition at line 271 of file gotoh_banded_inl.h.

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

• E:/git/nvbio/nvbio/alignment/gotoh/gotoh_banded_inl.h