template<
uint32 BAND_LEN,
AlignmentType TYPE,
typename algorithm_tag,
typename checkpoint_type = PatternBlockingTag>
struct nvbio::aln::priv::SWCheckpointedScoringContext< BAND_LEN, TYPE, algorithm_tag, checkpoint_type >
A helper checkpointed-scoring context class for sw_alignment_score_dispatch which allows to perform scoring in multiple passes, saving & restoring a checkpoint each time.
Definition at line 132 of file sw_inl.h.
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NVBIO_FORCEINLINE NVBIO_HOST_DEVICE | SWCheckpointedScoringContext (checkpoint_type checkpoint) |
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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) |
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template<typename column_type > |
NVBIO_FORCEINLINE
NVBIO_HOST_DEVICE void | previous_column (const uint32 j, const uint32 N, const column_type column) |
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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) |
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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) |
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template<uint32 BAND_LEN, AlignmentType TYPE, typename algorithm_tag, typename checkpoint_type = PatternBlockingTag>
template<typename column_type , typename scoring_type , typename score_type >
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 150 of file sw_inl.h.