NVBIO
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Definition at line 1524 of file gotoh_inl.h.
#include <gotoh_inl.h>
Public Types | |
typedef GotohAligner< TYPE, scoring_type, algorithm_tag > | aligner_type |
Static Public Methods | |
template<typename sink_type > | |
NVBIO_FORCEINLINE static NVBIO_HOST_DEVICE bool | dispatch (const aligner_type aligner, const pattern_string pattern, const qual_string quals, const text_string text, const int32 min_score, sink_type &sink, column_type column) |
template<typename sink_type , typename checkpoint_type > | |
NVBIO_FORCEINLINE static NVBIO_HOST_DEVICE bool | dispatch (const aligner_type aligner, const pattern_string pattern, const qual_string quals, const text_string text, const int32 min_score, const uint32 window_begin, const uint32 window_end, sink_type &sink, checkpoint_type checkpoint, column_type column) |
template<typename sink_type > | |
NVBIO_FORCEINLINE static NVBIO_HOST_DEVICE bool | dispatch (const aligner_type aligner, const pattern_string pattern, const qual_string quals, const text_string text, const int32 min_score, const uint32 window_begin, const uint32 window_end, sink_type &sink, column_type column) |
typedef GotohAligner<TYPE,scoring_type,algorithm_tag> nvbio::aln::priv::alignment_score_dispatch< GotohAligner< TYPE, scoring_type, algorithm_tag >, pattern_string, qual_string, text_string, column_type >::aligner_type |
Definition at line 1531 of file gotoh_inl.h.
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inlinestatic |
dispatch scoring across the whole pattern
aligner | scoring scheme |
pattern | pattern string (horizontal) |
quals | pattern qualities |
text | text string (vertical) |
min_score | minimum score |
sink | output alignment sink |
column | temporary column storage |
Definition at line 1548 of file gotoh_inl.h.
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inlinestatic |
dispatch scoring in a window of the pattern
checkpoint_type | a class to represent the checkpoint: an array of size equal to the text, that has to provide the const indexing operator[]. |
aligner | scoring scheme |
pattern | pattern string (horizontal) |
quals | pattern qualities |
text | text string (vertical) |
min_score | minimum score |
sink | output alignment sink |
column | temporary column storage |
Definition at line 1587 of file gotoh_inl.h.
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inlinestatic |
dispatch scoring in a window of the pattern, retaining the intermediate results in the column vector, essentially used as a continuation
aligner | scoring scheme |
pattern | pattern string (horizontal) |
quals | pattern qualities |
text | text string (vertical) |
min_score | minimum score |
sink | output alignment sink |
column | temporary column storage |
Definition at line 1623 of file gotoh_inl.h.