Detailed description

template< AlignmentType T_TYPE, typename scoring_scheme_type, typename AlgorithmType = PatternBlockingTag>
struct nvbio::aln::SmithWatermanAligner< T_TYPE, scoring_scheme_type, AlgorithmType >

A Smith-Waterman alignment algorithm, see Aligners

Template Parameters

TYPE	specifies whether the alignment is LOCAL/SEMI_GLOBAL/GLOBAL
scoring_scheme_type	specifies the scoring scheme, a model of Smith-Waterman Scoring Scheme
AlgorithmType	specifies the Algorithm Tag

Smith-Waterman Scoring Scheme

A Smith-Waterman scoring scheme is a class exposing the following interface:

struct SmithWatermanScoringScheme
{
    // the match bonus at a given quality q 
    int32 match(const uint8 q = 0)      const;
    // the mismatch penalty at a given quality q 
    int32 mismatch(const uint8 q = 0)   const;
    // the text deletion penalty
    int32 deletion()                    const;
    // the text insertion penalty
    int32 insertion()                   const;
};

Definition at line 327 of file alignment_base.h.

#include <alignment_base.h>

Public Types
typedef SmithWatermanTag	aligner_tag
	the Aligner Tag More...

typedef AlgorithmType	algorithm_tag
	the Algorithm Tag More...

Public Methods
NVBIO_FORCEINLINE NVBIO_HOST_DEVICE	SmithWatermanAligner (const scoring_scheme_type _scheme)

Public Members
scoring_scheme_type	scheme

Static Public Members
static const AlignmentType	TYPE = T_TYPE
	the AlignmentType More...