nvbio::aln::BestColumnSink< ScoreType, N > Struct Template Reference

Detailed description

template< typename ScoreType, uint32 N = 16>
struct nvbio::aln::BestColumnSink< ScoreType, N >

A sink for valid alignments, mantaining the best alignments by "column", where columns have a specified width

Definition at line 149 of file sink.h.

#include <sink.h>

Public Methods
NVBIO_FORCEINLINE NVBIO_HOST_DEVICE	BestColumnSink (const uint32 column_width=50, const ScoreType min_score=Field_traits< ScoreType >::min())
NVBIO_FORCEINLINE NVBIO_HOST_DEVICE void	set_column_width (const uint32 column_width)
NVBIO_FORCEINLINE NVBIO_HOST_DEVICE void	set_min_score (const uint32 min_score)
NVBIO_FORCEINLINE NVBIO_HOST_DEVICE void	invalidate ()
NVBIO_FORCEINLINE NVBIO_HOST_DEVICE void	report (const ScoreType score, const uint2 sink)
NVBIO_FORCEINLINE NVBIO_HOST_DEVICE void	best2 (uint32 &i1, uint32 &i2, const uint32 min_dist) const

Public Members
ScoreType	scores [N+1]
uint2	sinks [N+1]

Constructor & Destructor Documentation

template<typename ScoreType , uint32 N>

NVBIO_FORCEINLINE NVBIO_HOST_DEVICE nvbio::aln::BestColumnSink< ScoreType, N >::BestColumnSink	(	const uint32	column_width = 50,
		const ScoreType	min_score = Field_traits<ScoreType>::min()
	)

constructor

Parameters

column_width

the width of each column

Definition at line 120 of file sink_inl.h.

Member Function Documentation

template<typename ScoreType , uint32 N>

NVBIO_FORCEINLINE NVBIO_HOST_DEVICE void nvbio::aln::BestColumnSink< ScoreType, N >::best2	(	uint32 &	i1,
		uint32 &	i2,
		const uint32	min_dist
	)		const

return the index of the best and second-best alignments

Definition at line 165 of file sink_inl.h.

template<typename ScoreType , uint32 N>

NVBIO_FORCEINLINE NVBIO_HOST_DEVICE void nvbio::aln::BestColumnSink< ScoreType, N >::invalidate

(

)

invalidate

Definition at line 131 of file sink_inl.h.

template<typename ScoreType , uint32 N>

NVBIO_FORCEINLINE NVBIO_HOST_DEVICE void nvbio::aln::BestColumnSink< ScoreType, N >::report	(	const ScoreType	score,
		const uint2	sink
	)

store a valid alignment

Parameters

score	alignment's score
sink	alignment's end

Definition at line 147 of file sink_inl.h.

template<typename ScoreType, uint32 N = 16>

NVBIO_FORCEINLINE NVBIO_HOST_DEVICE void nvbio::aln::BestColumnSink< ScoreType, N >::set_column_width ( const uint32  column_width)

inline

reset column width

Definition at line 160 of file sink.h.

template<typename ScoreType, uint32 N = 16>

NVBIO_FORCEINLINE NVBIO_HOST_DEVICE void nvbio::aln::BestColumnSink< ScoreType, N >::set_min_score ( const uint32  min_score)

inline

reset minimum score

Definition at line 165 of file sink.h.

Member Data Documentation

template<typename ScoreType, uint32 N = 16>

ScoreType nvbio::aln::BestColumnSink< ScoreType, N >::scores[N+1]

Definition at line 185 of file sink.h.

template<typename ScoreType, uint32 N = 16>

uint2 nvbio::aln::BestColumnSink< ScoreType, N >::sinks[N+1]

Definition at line 186 of file sink.h.

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

• E:/git/nvbio/nvbio/alignment/sink.h
• E:/git/nvbio/nvbio/alignment/sink_inl.h