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

Detailed description

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

A helper scoring context class, which can be used to adapt the basic hamming_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 56 of file hamming_inl.h.

#include <hamming_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::HammingScoringContext< 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
jcolumn index
Ncolumn size
columncolumn values
scoringscoring scheme
zerozero value

Definition at line 68 of file hamming_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::HammingScoringContext< 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
jcolumn index
Ncolumn size
columncolumn values

Definition at line 101 of file hamming_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::HammingScoringContext< 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
irow index
Nnumber of rows (column size)
jcolumn index
Mnumber of columns (row size)
scorecomputed score
dirdirection flow

Definition at line 117 of file hamming_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::HammingScoringContext< 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
jcolumn index
Ncolumn size
columncolumn values

Definition at line 89 of file hamming_inl.h.


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