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

Detailed description

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

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

Definition at line 279 of file gotoh_banded_inl.h.

#include <gotoh_banded_inl.h>

Public Methods

NVBIO_FORCEINLINE NVBIO_HOST_DEVICE GotohSubmatrixContext (const checkpoint_type checkpoints, const uint32 checkpoint_id, submatrix_type submatrix)
 
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 hdir, const DirectionVector edir, const DirectionVector fdir)
 

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::GotohSubmatrixContext< BAND_LEN, TYPE, CHECKPOINTS, checkpoint_type, submatrix_type >::GotohSubmatrixContext ( const checkpoint_type  checkpoints,
const uint32  checkpoint_id,
submatrix_type  submatrix 
)
inline

Definition at line 282 of file gotoh_banded_inl.h.

Member Function Documentation

template<uint32 BAND_LEN, AlignmentType TYPE, uint32 CHECKPOINTS, typename checkpoint_type, typename submatrix_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::GotohSubmatrixContext< BAND_LEN, TYPE, CHECKPOINTS, checkpoint_type, submatrix_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 292 of file gotoh_banded_inl.h.

template<uint32 BAND_LEN, AlignmentType TYPE, uint32 CHECKPOINTS, typename checkpoint_type, typename submatrix_type>
template<typename H_band_type , typename F_band_type >
NVBIO_FORCEINLINE NVBIO_HOST_DEVICE void nvbio::aln::priv::banded::GotohSubmatrixContext< BAND_LEN, TYPE, CHECKPOINTS, checkpoint_type, submatrix_type >::last_row ( const uint32  i,
const H_band_type &  H_band,
const F_band_type &  F_band 
)
inline

Definition at line 318 of file gotoh_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::GotohSubmatrixContext< BAND_LEN, TYPE, CHECKPOINTS, checkpoint_type, submatrix_type >::new_cell ( const uint32  i,
const uint32  j,
const score_type  score,
const DirectionVector  hdir,
const DirectionVector  edir,
const DirectionVector  fdir 
)
inline

Definition at line 325 of file gotoh_banded_inl.h.

template<uint32 BAND_LEN, AlignmentType TYPE, uint32 CHECKPOINTS, typename checkpoint_type, typename submatrix_type>
template<typename H_band_type , typename F_band_type >
NVBIO_FORCEINLINE NVBIO_HOST_DEVICE void nvbio::aln::priv::banded::GotohSubmatrixContext< BAND_LEN, TYPE, CHECKPOINTS, checkpoint_type, submatrix_type >::previous_row ( const uint32  i,
const H_band_type &  H_band,
const F_band_type &  F_band 
)
inline

Definition at line 311 of file gotoh_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::GotohSubmatrixContext< BAND_LEN, TYPE, CHECKPOINTS, checkpoint_type, submatrix_type >::m_checkpoint_id

Definition at line 342 of file gotoh_banded_inl.h.

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

Definition at line 341 of file gotoh_banded_inl.h.

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

Definition at line 343 of file gotoh_banded_inl.h.

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