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

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

Definition at line 167 of file sw_banded_inl.h.

#include <sw_banded_inl.h>

Public Methods

NVBIO_FORCEINLINE NVBIO_HOST_DEVICE SmithWatermanCheckpointContext (checkpoint_type checkpoints)
 
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
 

Constructor & Destructor Documentation

template<uint32 BAND_LEN, AlignmentType TYPE, uint32 CHECKPOINTS, typename checkpoint_type>
NVBIO_FORCEINLINE NVBIO_HOST_DEVICE nvbio::aln::priv::banded::SmithWatermanCheckpointContext< BAND_LEN, TYPE, CHECKPOINTS, checkpoint_type >::SmithWatermanCheckpointContext ( checkpoint_type  checkpoints)
inline

Definition at line 170 of file sw_banded_inl.h.

Member Function Documentation

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

Definition at line 175 of file sw_banded_inl.h.

template<uint32 BAND_LEN, AlignmentType TYPE, uint32 CHECKPOINTS, typename checkpoint_type>
template<typename band_type >
NVBIO_FORCEINLINE NVBIO_HOST_DEVICE void nvbio::aln::priv::banded::SmithWatermanCheckpointContext< BAND_LEN, TYPE, CHECKPOINTS, checkpoint_type >::last_row ( const uint32  i,
const band_type &  band 
)
inline

Definition at line 202 of file sw_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::SmithWatermanCheckpointContext< BAND_LEN, TYPE, CHECKPOINTS, checkpoint_type >::new_cell ( const uint32  i,
const uint32  j,
const score_type  score,
const DirectionVector  dir 
)
inline

Definition at line 217 of file sw_banded_inl.h.

template<uint32 BAND_LEN, AlignmentType TYPE, uint32 CHECKPOINTS, typename checkpoint_type>
template<typename band_type >
NVBIO_FORCEINLINE NVBIO_HOST_DEVICE void nvbio::aln::priv::banded::SmithWatermanCheckpointContext< BAND_LEN, TYPE, CHECKPOINTS, checkpoint_type >::previous_row ( const uint32  i,
const band_type &  band 
)
inline

Definition at line 186 of file sw_banded_inl.h.

Member Data Documentation

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

Definition at line 223 of file sw_banded_inl.h.


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