nvbio::SSA_value_multiple Struct Reference

Detailed description

Build a sampled suffix array storing only the values which are a multiple of K, i.e. { SA[i] | SA[i] % K = 0 }

Definition at line 134 of file ssa.h.

#include <ssa.h>

Public Types
typedef SSA_value_multiple_context < const uint32 *, const uint32 *, const uint32 * >	context_type
typedef SSA_value_multiple_device	device_type
typedef context_type	device_view_type
typedef context_type	plain_view_type

Public Methods
	SSA_value_multiple ()
	SSA_value_multiple (const uint32 n, const int32 *sa, const uint32 K)
template<typename FMIndexType >
	SSA_value_multiple (const FMIndexType &fmi, const uint32 K)
context_type	get_context () const

Public Members
uint32	m_n
uint32	m_stored
std::vector< uint32 >	m_ssa
std::vector< uint32 >	m_bitmask
std::vector< uint32 >	m_blocks

Member Typedef Documentation

typedef SSA_value_multiple_context< const uint32*, const uint32*, const uint32*> nvbio::SSA_value_multiple::context_type

Definition at line 139 of file ssa.h.

typedef SSA_value_multiple_device nvbio::SSA_value_multiple::device_type

Definition at line 140 of file ssa.h.

typedef context_type nvbio::SSA_value_multiple::device_view_type

Definition at line 141 of file ssa.h.

typedef context_type nvbio::SSA_value_multiple::plain_view_type

Definition at line 142 of file ssa.h.

Constructor & Destructor Documentation

nvbio::SSA_value_multiple::SSA_value_multiple ( )

inline

empty constructor

Definition at line 146 of file ssa.h.

nvbio::SSA_value_multiple::SSA_value_multiple ( const uint32  n, const int32 *  sa, const uint32  K  )

inline

constructor

Parameters

n	number of entries in the SA
sa	suffix array
K	compression factor

Definition at line 32 of file ssa_inl.h.

template<typename FMIndexType >

nvbio::SSA_value_multiple::SSA_value_multiple	(	const FMIndexType &	fmi,
		const uint32	K
	)

constructor

Parameters

fmi	FM index
K	compression factor

Definition at line 80 of file ssa_inl.h.

Member Function Documentation

context_type nvbio::SSA_value_multiple::get_context ( ) const

inline

get a context

Definition at line 169 of file ssa.h.

Member Data Documentation

std::vector<uint32> nvbio::SSA_value_multiple::m_bitmask

Definition at line 177 of file ssa.h.

std::vector<uint32> nvbio::SSA_value_multiple::m_blocks

Definition at line 178 of file ssa.h.

uint32 nvbio::SSA_value_multiple::m_n

Definition at line 174 of file ssa.h.

std::vector<uint32> nvbio::SSA_value_multiple::m_ssa

Definition at line 176 of file ssa.h.

uint32 nvbio::SSA_value_multiple::m_stored

Definition at line 175 of file ssa.h.

---

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

• E:/git/nvbio/nvbio/fmindex/ssa.h
• E:/git/nvbio/nvbio/fmindex/ssa_inl.h