nvbio::aln::priv::SWScoringContext< BAND_LEN, TYPE, algorithm_tag > Struct Template Reference

Detailed description

template< uint32 BAND_LEN, AlignmentType TYPE, typename algorithm_tag = PatternBlockingTag>
struct nvbio::aln::priv::SWScoringContext< BAND_LEN, TYPE, algorithm_tag >

A helper scoring context class, which can be used to adapt the basic sw_alignment_score_dispatch algorithm to various situations, such as: scoring scoring within a window (i.e. saving only the last band within the window) computing checkpoints computing a flow submatrix

Definition at line 55 of file sw_inl.h.

#include <sw_inl.h>

Public Methods
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)

Member Function Documentation

template<uint32 BAND_LEN, AlignmentType TYPE, typename algorithm_tag = PatternBlockingTag>

template<typename column_type , typename scoring_type , typename score_type >

NVBIO_FORCEINLINE NVBIO_HOST_DEVICE void nvbio::aln::priv::SWScoringContext< BAND_LEN, TYPE, algorithm_tag >::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 67 of file sw_inl.h.

template<uint32 BAND_LEN, AlignmentType TYPE, typename algorithm_tag = PatternBlockingTag>

template<typename column_type >

NVBIO_FORCEINLINE NVBIO_HOST_DEVICE void nvbio::aln::priv::SWScoringContext< BAND_LEN, TYPE, algorithm_tag >::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 102 of file sw_inl.h.

template<uint32 BAND_LEN, AlignmentType TYPE, typename algorithm_tag = PatternBlockingTag>

template<typename score_type >

NVBIO_FORCEINLINE NVBIO_HOST_DEVICE void nvbio::aln::priv::SWScoringContext< BAND_LEN, TYPE, algorithm_tag >::new_cell ( const uint32  i, const uint32  N, const uint32  j, const uint32  M, const score_type  score, const DirectionVector  dir  )

inline

do something with the newly computed cell

Parameters

i	row index
N	number of rows (column size)
j	column index
M	number of columns (row size)
score	computed score
dir	direction flow

Definition at line 118 of file sw_inl.h.

template<uint32 BAND_LEN, AlignmentType TYPE, typename algorithm_tag = PatternBlockingTag>

template<typename column_type >

NVBIO_FORCEINLINE NVBIO_HOST_DEVICE void nvbio::aln::priv::SWScoringContext< BAND_LEN, TYPE, algorithm_tag >::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 90 of file sw_inl.h.

---

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

• E:/git/nvbio/nvbio/alignment/sw/sw_inl.h