Detailed description

A simple implementation of the Smith-Waterman Scoring Scheme model

Definition at line 92 of file utils.h.

#include <utils.h>

Public Methods
NVBIO_FORCEINLINE NVBIO_HOST_DEVICE	SimpleSmithWatermanScheme ()

NVBIO_FORCEINLINE NVBIO_HOST_DEVICE	SimpleSmithWatermanScheme (const int32 match, const int32 mm, const int32 del, const int32 ins)

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	deletion () const

NVBIO_FORCEINLINE NVBIO_HOST_DEVICE int32	insertion () const

Constructor & Destructor Documentation

NVBIO_FORCEINLINE NVBIO_HOST_DEVICE nvbio::aln::SimpleSmithWatermanScheme::SimpleSmithWatermanScheme ( )

inline

Definition at line 94 of file utils.h.

NVBIO_FORCEINLINE NVBIO_HOST_DEVICE nvbio::aln::SimpleSmithWatermanScheme::SimpleSmithWatermanScheme	(	const int32	match,
		const int32	mm,
		const int32	del,
		const int32	ins
	)

inline

Definition at line 95 of file utils.h.

NVBIO_FORCEINLINE NVBIO_HOST_DEVICE int32 nvbio::aln::SimpleSmithWatermanScheme::deletion ( ) const

inline

Definition at line 102 of file utils.h.

NVBIO_FORCEINLINE NVBIO_HOST_DEVICE int32 nvbio::aln::SimpleSmithWatermanScheme::insertion ( ) const

inline

Definition at line 103 of file utils.h.

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

inline

Definition at line 99 of file utils.h.

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

inline

Definition at line 100 of file utils.h.

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

inline

Definition at line 101 of file utils.h.

int32 nvbio::aln::SimpleSmithWatermanScheme::m_deletion

Definition at line 107 of file utils.h.

int32 nvbio::aln::SimpleSmithWatermanScheme::m_insertion

Definition at line 108 of file utils.h.

int32 nvbio::aln::SimpleSmithWatermanScheme::m_match

Definition at line 103 of file utils.h.

int32 nvbio::aln::SimpleSmithWatermanScheme::m_mismatch

Definition at line 106 of file utils.h.

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