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nvbio::aln::priv::GotohSubmatrixContext< 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::GotohSubmatrixContext< BAND_LEN, TYPE, CHECKPOINTS, checkpoint_type, submatrix_type >

Definition at line 348 of file gotoh_inl.h.

#include <gotoh_inl.h>

Public Methods

NVBIO_FORCEINLINE NVBIO_HOST_DEVICE GotohSubmatrixContext (const checkpoint_type checkpoints, const uint32 checkpoint_id, const submatrix_type submatrix)
 
template<typename column_type , typename scoring_type , typename score_type >
NVBIO_FORCEINLINE
NVBIO_HOST_DEVICE void 		init (const uint32 j, const uint32 N, column_type &column, const scoring_type &scoring, const score_type zero, const score_type infimum)
 
template<typename column_type >
NVBIO_FORCEINLINE
NVBIO_HOST_DEVICE void 		previous_column (const uint32 j, const uint32 N, const column_type column)
 
template<typename column_type >
NVBIO_FORCEINLINE
NVBIO_HOST_DEVICE void 		last_column (const uint32 j, const uint32 M, const uint32 N, const column_type column)
 
template<typename score_type >
NVBIO_FORCEINLINE
NVBIO_HOST_DEVICE void 		new_cell (const uint32 i, const uint32 N, const uint32 j, const uint32 M, 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::GotohSubmatrixContext< BAND_LEN, TYPE, CHECKPOINTS, checkpoint_type, submatrix_type >::GotohSubmatrixContext ( const checkpoint_type  checkpoints,
const uint32  checkpoint_id,
const submatrix_type  submatrix 
)
inline

Definition at line 356 of file gotoh_inl.h.

Member Function Documentation

template<uint32 BAND_LEN, AlignmentType TYPE, uint32 CHECKPOINTS, typename checkpoint_type, typename submatrix_type>
template<typename column_type , typename scoring_type , typename score_type >
NVBIO_FORCEINLINE NVBIO_HOST_DEVICE void nvbio::aln::priv::GotohSubmatrixContext< BAND_LEN, TYPE, CHECKPOINTS, checkpoint_type, submatrix_type >::init ( const uint32  j,
const uint32  N,
column_type &  column,
const scoring_type &  scoring,
const score_type  zero,
const score_type  infimum 
)
inline

Definition at line 374 of file gotoh_inl.h.

template<uint32 BAND_LEN, AlignmentType TYPE, uint32 CHECKPOINTS, typename checkpoint_type, typename submatrix_type>
template<typename column_type >
NVBIO_FORCEINLINE NVBIO_HOST_DEVICE void nvbio::aln::priv::GotohSubmatrixContext< BAND_LEN, TYPE, CHECKPOINTS, checkpoint_type, submatrix_type >::last_column ( const uint32  j,
const uint32  M,
const uint32  N,
const column_type  column 
)
inline

Definition at line 412 of file gotoh_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::GotohSubmatrixContext< BAND_LEN, TYPE, CHECKPOINTS, checkpoint_type, submatrix_type >::new_cell ( const uint32  i,
const uint32  N,
const uint32  j,
const uint32  M,
const score_type  score,
const DirectionVector  hdir,
const DirectionVector  edir,
const DirectionVector  fdir 
)
inline

Definition at line 428 of file gotoh_inl.h.

template<uint32 BAND_LEN, AlignmentType TYPE, uint32 CHECKPOINTS, typename checkpoint_type, typename submatrix_type>
template<typename column_type >
NVBIO_FORCEINLINE NVBIO_HOST_DEVICE void nvbio::aln::priv::GotohSubmatrixContext< BAND_LEN, TYPE, CHECKPOINTS, checkpoint_type, submatrix_type >::previous_column ( const uint32  j,
const uint32  N,
const column_type  column 
)
inline

Definition at line 400 of file gotoh_inl.h.

Member Data Documentation

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

Definition at line 448 of file gotoh_inl.h.

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

Definition at line 447 of file gotoh_inl.h.

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

Definition at line 449 of file gotoh_inl.h.

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