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

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

Definition at line 312 of file hamming_inl.h.

#include <hamming_inl.h>

Public Methods
NVBIO_FORCEINLINE NVBIO_HOST_DEVICE	HammingSubmatrixContext (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)
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 dir)

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

inline

Definition at line 315 of file hamming_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::HammingSubmatrixContext< 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  )

inline

initialize the j-th column of the DP matrix

Parameters

j	column index
N	column size
column	column values
scoring	scoring scheme
zero	zero value

Definition at line 332 of file hamming_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::HammingSubmatrixContext< BAND_LEN, TYPE, CHECKPOINTS, checkpoint_type, submatrix_type >::last_column ( const uint32  j, const uint32  M, const uint32  N, const column_type  column  )

inline

do something with the last column

Parameters

j	column index
N	column size
column	column values

Definition at line 363 of file hamming_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::HammingSubmatrixContext< 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  dir  )

inline

Definition at line 379 of file hamming_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::HammingSubmatrixContext< BAND_LEN, TYPE, CHECKPOINTS, checkpoint_type, submatrix_type >::previous_column ( const uint32  j, const uint32  N, const column_type  column  )

inline

do something with the previous column

Parameters

j	column index
N	column size
column	column values

Definition at line 351 of file hamming_inl.h.

Member Data Documentation

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

uint32 nvbio::aln::priv::HammingSubmatrixContext< BAND_LEN, TYPE, CHECKPOINTS, checkpoint_type, submatrix_type >::m_checkpoint_id

Definition at line 397 of file hamming_inl.h.

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

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

Definition at line 396 of file hamming_inl.h.

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

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

Definition at line 398 of file hamming_inl.h.

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

• E:/git/nvbio/nvbio/alignment/hamming/hamming_inl.h