nvbio::io::BestAlignments Struct Reference

Detailed description

A simple data-structure to hold the best 2 alignments

Definition at line 144 of file alignments.h.

#include <alignments.h>

Public Methods
NVBIO_HOST_DEVICE NVBIO_FORCEINLINE	BestAlignments ()
NVBIO_HOST_DEVICE NVBIO_FORCEINLINE	BestAlignments (const Alignment &a1, const Alignment &a2)
NVBIO_HOST_DEVICE NVBIO_FORCEINLINE bool	is_aligned () const
NVBIO_HOST_DEVICE NVBIO_FORCEINLINE bool	has_second () const
NVBIO_HOST_DEVICE NVBIO_FORCEINLINE int32	best_score () const
NVBIO_HOST_DEVICE NVBIO_FORCEINLINE uint32	best_ed () const
NVBIO_HOST_DEVICE NVBIO_FORCEINLINE uint32	best_alignment_pos () const
NVBIO_HOST_DEVICE NVBIO_FORCEINLINE int32	second_score () const
NVBIO_HOST_DEVICE NVBIO_FORCEINLINE uint32	second_ed () const
NVBIO_HOST_DEVICE NVBIO_FORCEINLINE uint32	second_alignment_pos () const
NVBIO_HOST_DEVICE NVBIO_FORCEINLINE const Alignment &	best () const
NVBIO_HOST_DEVICE NVBIO_FORCEINLINE const Alignment &	second_best () const
template<uint32 I>
NVBIO_HOST_DEVICE NVBIO_FORCEINLINE const Alignment &	alignment () const
template<uint32 I>
NVBIO_HOST_DEVICE NVBIO_FORCEINLINE Alignment &	alignment ()
template<uint32 I>
NVBIO_HOST_DEVICE NVBIO_FORCEINLINE uint32	alignment_pos () const
template<uint32 I>
NVBIO_HOST_DEVICE NVBIO_FORCEINLINE int32	score () const
template<uint32 I>
NVBIO_HOST_DEVICE NVBIO_FORCEINLINE uint32	ed () const
template<uint32 I>
NVBIO_HOST_DEVICE NVBIO_FORCEINLINE bool	is_aligned () const
template<uint32 I>
NVBIO_HOST_DEVICE NVBIO_FORCEINLINE bool	is_rc () const

Public Members
Alignment	m_a1
Alignment	m_a2

Constructor & Destructor Documentation

NVBIO_HOST_DEVICE NVBIO_FORCEINLINE nvbio::io::BestAlignments::BestAlignments ( )

inline

Definition at line 147 of file alignments.h.

NVBIO_HOST_DEVICE NVBIO_FORCEINLINE nvbio::io::BestAlignments::BestAlignments ( const Alignment &  a1, const Alignment &  a2  )

inline

Definition at line 150 of file alignments.h.

Member Function Documentation

template<uint32 I>

NVBIO_HOST_DEVICE NVBIO_FORCEINLINE const Alignment& nvbio::io::BestAlignments::alignment ( ) const

inline

Definition at line 166 of file alignments.h.

template<uint32 I>

NVBIO_HOST_DEVICE NVBIO_FORCEINLINE Alignment& nvbio::io::BestAlignments::alignment ( )

inline

Definition at line 170 of file alignments.h.

template<uint32 I>

NVBIO_HOST_DEVICE NVBIO_FORCEINLINE uint32 nvbio::io::BestAlignments::alignment_pos ( ) const

inline

Definition at line 174 of file alignments.h.

NVBIO_HOST_DEVICE NVBIO_FORCEINLINE const Alignment& nvbio::io::BestAlignments::best ( ) const

inline

Definition at line 161 of file alignments.h.

NVBIO_HOST_DEVICE NVBIO_FORCEINLINE uint32 nvbio::io::BestAlignments::best_alignment_pos ( ) const

inline

Definition at line 156 of file alignments.h.

NVBIO_HOST_DEVICE NVBIO_FORCEINLINE uint32 nvbio::io::BestAlignments::best_ed ( ) const

inline

Definition at line 155 of file alignments.h.

NVBIO_HOST_DEVICE NVBIO_FORCEINLINE int32 nvbio::io::BestAlignments::best_score ( ) const

inline

Definition at line 154 of file alignments.h.

template<uint32 I>

NVBIO_HOST_DEVICE NVBIO_FORCEINLINE uint32 nvbio::io::BestAlignments::ed ( ) const

inline

Definition at line 182 of file alignments.h.

NVBIO_HOST_DEVICE NVBIO_FORCEINLINE bool nvbio::io::BestAlignments::has_second ( ) const

inline

Definition at line 153 of file alignments.h.

NVBIO_HOST_DEVICE NVBIO_FORCEINLINE bool nvbio::io::BestAlignments::is_aligned ( ) const

inline

Definition at line 152 of file alignments.h.

template<uint32 I>

NVBIO_HOST_DEVICE NVBIO_FORCEINLINE bool nvbio::io::BestAlignments::is_aligned ( ) const

inline

Definition at line 186 of file alignments.h.

template<uint32 I>

NVBIO_HOST_DEVICE NVBIO_FORCEINLINE bool nvbio::io::BestAlignments::is_rc ( ) const

inline

Definition at line 190 of file alignments.h.

template<uint32 I>

NVBIO_HOST_DEVICE NVBIO_FORCEINLINE int32 nvbio::io::BestAlignments::score ( ) const

inline

Definition at line 178 of file alignments.h.

NVBIO_HOST_DEVICE NVBIO_FORCEINLINE uint32 nvbio::io::BestAlignments::second_alignment_pos ( ) const

inline

Definition at line 159 of file alignments.h.

NVBIO_HOST_DEVICE NVBIO_FORCEINLINE const Alignment& nvbio::io::BestAlignments::second_best ( ) const

inline

Definition at line 162 of file alignments.h.

NVBIO_HOST_DEVICE NVBIO_FORCEINLINE uint32 nvbio::io::BestAlignments::second_ed ( ) const

inline

Definition at line 158 of file alignments.h.

NVBIO_HOST_DEVICE NVBIO_FORCEINLINE int32 nvbio::io::BestAlignments::second_score ( ) const

inline

Definition at line 157 of file alignments.h.

Member Data Documentation

Alignment nvbio::io::BestAlignments::m_a1

Definition at line 192 of file alignments.h.

Alignment nvbio::io::BestAlignments::m_a2

Definition at line 193 of file alignments.h.

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

• E:/git/nvbio/nvbio/io/alignments.h