Detailed description

Definition at line 628 of file alignment_test_utils.h.

Public Methods
void	clear ()

NVBIO_HOST_DEVICE void	clip (const uint32 len)

NVBIO_HOST_DEVICE void	push (const uint8 op)

template<AlignmentType TYPE>
int32	score (EditDistanceAligner< TYPE > aligner, const uint32 offset, const uint8 str, const uint8 ref)

template<AlignmentType TYPE, typename scoring_type >
int32	score (SmithWatermanAligner< TYPE, scoring_type > aligner, const uint32 offset, const uint8 str, const uint8 ref)

template<AlignmentType TYPE, typename scoring_type >
int32	score (GotohAligner< TYPE, scoring_type > aligner, const uint32 offset, const uint8 str, const uint8 ref)

Member Function Documentation

void nvbio::aln::TestBacktracker::clear ( void )

inline

Definition at line 630 of file alignment_test_utils.h.

NVBIO_HOST_DEVICE void nvbio::aln::TestBacktracker::clip ( const uint32 len)

inline

Definition at line 633 of file alignment_test_utils.h.

NVBIO_HOST_DEVICE void nvbio::aln::TestBacktracker::push ( const uint8 op)

inline

Definition at line 640 of file alignment_test_utils.h.

template<AlignmentType TYPE>

int32 nvbio::aln::TestBacktracker::score	(	EditDistanceAligner< TYPE >	aligner,
		const uint32	offset,
		const uint8 *	str,
		const uint8 *	ref
	)

inline

Definition at line 648 of file alignment_test_utils.h.

template<AlignmentType TYPE, typename scoring_type >

int32 nvbio::aln::TestBacktracker::score	(	SmithWatermanAligner< TYPE, scoring_type >	aligner,
		const uint32	offset,
		const uint8 *	str,
		const uint8 *	ref
	)

inline

Definition at line 693 of file alignment_test_utils.h.

template<AlignmentType TYPE, typename scoring_type >

int32 nvbio::aln::TestBacktracker::score	(	GotohAligner< TYPE, scoring_type >	aligner,
		const uint32	offset,
		const uint8 *	str,
		const uint8 *	ref
	)

inline

Definition at line 740 of file alignment_test_utils.h.

char nvbio::aln::TestBacktracker::aln[1024]

Definition at line 788 of file alignment_test_utils.h.

uint32 nvbio::aln::TestBacktracker::aln_len

Definition at line 789 of file alignment_test_utils.h.

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