NVBIO
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A helper checkpointed-scoring context class for hamming_alignment_score_dispatch which allows to perform scoring in multiple passes, saving & restoring a checkpoint each time.
Definition at line 131 of file hamming_inl.h.
#include <hamming_inl.h>
Public Methods | |
NVBIO_FORCEINLINE NVBIO_HOST_DEVICE | HammingCheckpointedScoringContext (checkpoint_type checkpoint) |
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_checkpoint |
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Definition at line 137 of file hamming_inl.h.
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initialize the j-th column of the DP matrix
j | column index |
N | column size |
column | column values |
scoring | scoring scheme |
zero | zero value |
Definition at line 149 of file hamming_inl.h.
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do something with the last column
j | column index |
N | column size |
column | column values |
Definition at line 187 of file hamming_inl.h.
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do something with the newly computed cell
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 210 of file hamming_inl.h.
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do something with the previous column
j | column index |
N | column size |
column | column values |
Definition at line 175 of file hamming_inl.h.
checkpoint_type nvbio::aln::priv::HammingCheckpointedScoringContext< BAND_LEN, TYPE, algorithm_tag, checkpoint_type >::m_checkpoint |
Definition at line 218 of file hamming_inl.h.