Detailed description

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

A Gotoh alignment algorithm, see Aligners

Template Parameters

T_TYPE	specifies whether the alignment is LOCAL/SEMI_GLOBAL/GLOBAL
scoring_scheme_type	specifies the scoring scheme, a model of Gotoh Scoring Scheme
AlgorithmType	specifies the Algorithm Tag

Gotoh Scoring Scheme

A Gotoh scoring scheme is a class exposing the following interface:

struct GotohScoringScheme
{
    // the maximum match bonus at a given quality q 
    int32 match(const uint8 q = 0) const;
    // the substitution score of text and pattern bases (t,p),
    // at positions (t_i,p_j), with a given pattern quality q
    int32 substitution(
        const uint32 t_i, const uint32 p_j,
        const uint8  t,   const uint8  p,   const uint8 q = 0) const;
    // the pattern gap open cost
    int32 pattern_gap_open()       const;
    // the pattern gap extension cost
    int32 pattern_gap_extension()  const;
    // the text gap open cost
    int32 text_gap_open()          const;
    // the text gap extension cost
    int32 text_gap_extension()     const;
};

Definition at line 256 of file alignment_base.h.

#include <alignment_base.h>

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

typedef AlgorithmType	algorithm_tag
	the Algorithm Tag More...

Public Methods
NVBIO_FORCEINLINE NVBIO_HOST_DEVICE	GotohAligner (const scoring_scheme_type _scheme)

Public Members
scoring_scheme_type	scheme

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