nvbio::aln::SimpleGotohScheme Struct Reference

Detailed description

A simple implementation of the Gotoh Scoring Scheme model

Definition at line 114 of file utils.h.

#include <utils.h>

Public Methods
NVBIO_FORCEINLINE NVBIO_HOST_DEVICE	SimpleGotohScheme ()
NVBIO_FORCEINLINE NVBIO_HOST_DEVICE	SimpleGotohScheme (const int32 match, const int32 mm, const int32 gap_open, const int32 gap_ext)
NVBIO_FORCEINLINE NVBIO_HOST_DEVICE int32	match (const uint8 q=0) const
NVBIO_FORCEINLINE NVBIO_HOST_DEVICE int32	mismatch (const uint8 q=0) const
NVBIO_FORCEINLINE NVBIO_HOST_DEVICE int32	mismatch (const uint8 a, const uint8 b, const uint8 q=0) const
NVBIO_FORCEINLINE NVBIO_HOST_DEVICE int32	substitution (const uint32 r_i, const uint32 q_j, const uint8 r, const uint8 q, const uint8 qq=0) const
NVBIO_FORCEINLINE NVBIO_HOST_DEVICE int32	pattern_gap_open () const
NVBIO_FORCEINLINE NVBIO_HOST_DEVICE int32	pattern_gap_extension () const
NVBIO_FORCEINLINE NVBIO_HOST_DEVICE int32	text_gap_open () const
NVBIO_FORCEINLINE NVBIO_HOST_DEVICE int32	text_gap_extension () const

Public Members
int32	m_match
int32	m_mismatch
int32	m_gap_open
int32	m_gap_ext

Constructor & Destructor Documentation

NVBIO_FORCEINLINE NVBIO_HOST_DEVICE nvbio::aln::SimpleGotohScheme::SimpleGotohScheme ( )

inline

Definition at line 116 of file utils.h.

NVBIO_FORCEINLINE NVBIO_HOST_DEVICE nvbio::aln::SimpleGotohScheme::SimpleGotohScheme ( const int32  match, const int32  mm, const int32  gap_open, const int32  gap_ext  )

inline

Definition at line 117 of file utils.h.

Member Function Documentation

NVBIO_FORCEINLINE NVBIO_HOST_DEVICE int32 nvbio::aln::SimpleGotohScheme::match ( const uint8  q = 0) const

inline

Definition at line 121 of file utils.h.

NVBIO_FORCEINLINE NVBIO_HOST_DEVICE int32 nvbio::aln::SimpleGotohScheme::mismatch ( const uint8  q = 0) const

inline

Definition at line 122 of file utils.h.

NVBIO_FORCEINLINE NVBIO_HOST_DEVICE int32 nvbio::aln::SimpleGotohScheme::mismatch ( const uint8  a, const uint8  b, const uint8  q = 0  ) const

inline

Definition at line 123 of file utils.h.

NVBIO_FORCEINLINE NVBIO_HOST_DEVICE int32 nvbio::aln::SimpleGotohScheme::pattern_gap_extension ( ) const

inline

Definition at line 126 of file utils.h.

NVBIO_FORCEINLINE NVBIO_HOST_DEVICE int32 nvbio::aln::SimpleGotohScheme::pattern_gap_open ( ) const

inline

Definition at line 125 of file utils.h.

NVBIO_FORCEINLINE NVBIO_HOST_DEVICE int32 nvbio::aln::SimpleGotohScheme::substitution ( const uint32  r_i, const uint32  q_j, const uint8  r, const uint8  q, const uint8  qq = 0  ) const

inline

Definition at line 124 of file utils.h.

NVBIO_FORCEINLINE NVBIO_HOST_DEVICE int32 nvbio::aln::SimpleGotohScheme::text_gap_extension ( ) const

inline

Definition at line 128 of file utils.h.

NVBIO_FORCEINLINE NVBIO_HOST_DEVICE int32 nvbio::aln::SimpleGotohScheme::text_gap_open ( ) const

inline

Definition at line 127 of file utils.h.

Member Data Documentation

int32 nvbio::aln::SimpleGotohScheme::m_gap_ext

Definition at line 133 of file utils.h.

int32 nvbio::aln::SimpleGotohScheme::m_gap_open

Definition at line 132 of file utils.h.

int32 nvbio::aln::SimpleGotohScheme::m_match

Definition at line 128 of file utils.h.

int32 nvbio::aln::SimpleGotohScheme::m_mismatch

Definition at line 131 of file utils.h.

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

• E:/git/nvbio/nvbio/alignment/utils.h