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nvbio::aln::priv::alignment_score_dispatch< EditDistanceAligner< TYPE, algorithm_tag >, pattern_string, qual_string, text_string, column_type > Struct Template Reference

Detailed description

template< AlignmentType TYPE, typename algorithm_tag, typename pattern_string, typename qual_string, typename text_string, typename column_type>
struct nvbio::aln::priv::alignment_score_dispatch< EditDistanceAligner< TYPE, algorithm_tag >, pattern_string, qual_string, text_string, column_type >

Calculate the alignment score between a pattern and a text, using the Smith-Waterman algorithm.

Template Parameters
TYPEthe alignment type
pattern_stringpattern string
quals_stringpattern qualities
text_stringtext string
column_typetemporary column storage

Definition at line 62 of file ed_inl.h.

#include <ed_inl.h>

Public Types

typedef EditDistanceAligner
< 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)
 

Member Typedef Documentation

template<AlignmentType TYPE, typename algorithm_tag , typename pattern_string , typename qual_string , typename text_string , typename column_type >
typedef EditDistanceAligner<TYPE,algorithm_tag> nvbio::aln::priv::alignment_score_dispatch< EditDistanceAligner< TYPE, algorithm_tag >, pattern_string, qual_string, text_string, column_type >::aligner_type

Definition at line 69 of file ed_inl.h.

Member Function Documentation

template<AlignmentType TYPE, typename algorithm_tag , typename pattern_string , typename qual_string , typename text_string , typename column_type >
template<typename sink_type >
NVBIO_FORCEINLINE static NVBIO_HOST_DEVICE bool nvbio::aln::priv::alignment_score_dispatch< EditDistanceAligner< TYPE, algorithm_tag >, pattern_string, qual_string, text_string, column_type >::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 
)
inlinestatic

dispatch scoring across the whole pattern

Parameters
alignerscoring scheme
patternpattern string (horizontal
qualspattern qualities
texttext string (vertical)
min_scoreminimum score
sinkoutput alignment sink
Returns
true iff the minimum score was reached

Definition at line 84 of file ed_inl.h.

template<AlignmentType TYPE, typename algorithm_tag , typename pattern_string , typename qual_string , typename text_string , typename column_type >
template<typename sink_type , typename checkpoint_type >
NVBIO_FORCEINLINE static NVBIO_HOST_DEVICE bool nvbio::aln::priv::alignment_score_dispatch< EditDistanceAligner< TYPE, algorithm_tag >, pattern_string, qual_string, text_string, column_type >::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 
)
inlinestatic

dispatch scoring in a window of the pattern

Template Parameters
checkpoint_typea class to represent the checkpoint: an array of size equal to the text, that has to provide the const indexing operator[].
Parameters
alignerscoring scheme
patternpattern string (horizontal
qualspattern qualities
texttext string (vertical)
min_scoreminimum score
sinkoutput alignment sink
checkpointin/out checkpoint
Returns
true iff the minimum score was reached

Definition at line 123 of file ed_inl.h.

template<AlignmentType TYPE, typename algorithm_tag , typename pattern_string , typename qual_string , typename text_string , typename column_type >
template<typename sink_type >
NVBIO_FORCEINLINE static NVBIO_HOST_DEVICE bool nvbio::aln::priv::alignment_score_dispatch< EditDistanceAligner< TYPE, algorithm_tag >, pattern_string, qual_string, text_string, column_type >::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 
)
inlinestatic

dispatch scoring in a window of the pattern, retaining the intermediate results in the column vector, essentially used as a continuation

Parameters
alignerscoring scheme
patternpattern string (horizontal
qualspattern qualities
texttext string (vertical)
min_scoreminimum score
sinkoutput alignment sink
Returns
true iff the minimum score was reached

Definition at line 158 of file ed_inl.h.


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