nvbio::TrieNode< ALPHABET_SIZE_T, TYPE_T > Struct Template Reference

Detailed description

template< uint32 ALPHABET_SIZE_T, TrieType TYPE_T>
struct nvbio::TrieNode< ALPHABET_SIZE_T, TYPE_T >

A suffix trie node

Template Parameters

ALPHABET_SIZE_T

the size of the alphabet, in symbols

TYPE_T

a suffix trie can be stored either with an uncompressed layout, where each inner node reseves storage for |alphabet| children and some of them are marked as invalid, or with a compressed one, where only storage for the active children is actually reserved; the latter type requires just a little more logic during traversal, as a popcount is necessary to select the child corresponding to the i-th character.

Definition at line 77 of file suffix_trie.h.

#include <suffix_trie.h>

Public Methods
NVBIO_FORCEINLINE NVBIO_HOST_DEVICE	TrieNode ()
NVBIO_FORCEINLINE NVBIO_HOST_DEVICE	TrieNode (const uint32 _child, const uint32 _mask)
NVBIO_FORCEINLINE NVBIO_HOST_DEVICE bool	is_leaf () const
NVBIO_FORCEINLINE NVBIO_HOST_DEVICE uint32	child () const
NVBIO_FORCEINLINE NVBIO_HOST_DEVICE uint32	child (const uint32 c) const
NVBIO_FORCEINLINE NVBIO_HOST_DEVICE uint32	nth_child (const uint32 c) const
NVBIO_FORCEINLINE NVBIO_HOST_DEVICE uint32	first_child () const
NVBIO_FORCEINLINE NVBIO_HOST_DEVICE uint32	mask () const
NVBIO_FORCEINLINE NVBIO_HOST_DEVICE void	set_child_bit (const uint32 c)
NVBIO_FORCEINLINE NVBIO_HOST_DEVICE uint32	child_bit (const uint32 c) const
NVBIO_FORCEINLINE NVBIO_HOST_DEVICE void	set_size (const uint32 size)
NVBIO_FORCEINLINE NVBIO_HOST_DEVICE uint32	size () const

Public Members
uint32	m_child
uint32	m_mask
uint32	m_size

Static Public Members
static const uint32	ALPHABET_SIZE = ALPHABET_SIZE_T
static const uint32	invalid_node = uint32(-1)
static const TrieType	trie_type = TYPE_T

Constructor & Destructor Documentation

template<uint32 ALPHABET_SIZE_T, TrieType TYPE_T>

NVBIO_FORCEINLINE NVBIO_HOST_DEVICE nvbio::TrieNode< ALPHABET_SIZE_T, TYPE_T >::TrieNode

(

)

Definition at line 37 of file suffix_trie_inl.h.

template<uint32 ALPHABET_SIZE_T, TrieType TYPE_T>

NVBIO_FORCEINLINE NVBIO_HOST_DEVICE nvbio::TrieNode< ALPHABET_SIZE_T, TYPE_T >::TrieNode	(	const uint32	_child,
		const uint32	_mask
	)

Definition at line 41 of file suffix_trie_inl.h.

Member Function Documentation

template<uint32 ALPHABET_SIZE_T, TrieType TYPE_T>

NVBIO_FORCEINLINE NVBIO_HOST_DEVICE uint32 nvbio::TrieNode< ALPHABET_SIZE_T, TYPE_T >::child

(

)

const

Definition at line 53 of file suffix_trie_inl.h.

template<uint32 ALPHABET_SIZE_T, TrieType TYPE_T>

NVBIO_FORCEINLINE NVBIO_HOST_DEVICE uint32 nvbio::TrieNode< ALPHABET_SIZE_T, TYPE_T >::child

(

const uint32

c)

const

Definition at line 57 of file suffix_trie_inl.h.

template<uint32 ALPHABET_SIZE_T, TrieType TYPE_T>

NVBIO_FORCEINLINE NVBIO_HOST_DEVICE uint32 nvbio::TrieNode< ALPHABET_SIZE_T, TYPE_T >::child_bit

(

const uint32

c)

const

Definition at line 95 of file suffix_trie_inl.h.

template<uint32 ALPHABET_SIZE_T, TrieType TYPE_T>

NVBIO_FORCEINLINE NVBIO_HOST_DEVICE uint32 nvbio::TrieNode< ALPHABET_SIZE_T, TYPE_T >::first_child

(

)

const

Definition at line 77 of file suffix_trie_inl.h.

template<uint32 ALPHABET_SIZE_T, TrieType TYPE_T>

NVBIO_FORCEINLINE NVBIO_HOST_DEVICE bool nvbio::TrieNode< ALPHABET_SIZE_T, TYPE_T >::is_leaf

(

)

const

Definition at line 49 of file suffix_trie_inl.h.

template<uint32 ALPHABET_SIZE_T, TrieType TYPE_T>

NVBIO_FORCEINLINE NVBIO_HOST_DEVICE uint32 nvbio::TrieNode< ALPHABET_SIZE_T, TYPE_T >::mask

(

)

const

Definition at line 87 of file suffix_trie_inl.h.

template<uint32 ALPHABET_SIZE_T, TrieType TYPE_T>

NVBIO_FORCEINLINE NVBIO_HOST_DEVICE uint32 nvbio::TrieNode< ALPHABET_SIZE_T, TYPE_T >::nth_child

(

const uint32

c)

const

Definition at line 67 of file suffix_trie_inl.h.

template<uint32 ALPHABET_SIZE_T, TrieType TYPE_T>

NVBIO_FORCEINLINE NVBIO_HOST_DEVICE void nvbio::TrieNode< ALPHABET_SIZE_T, TYPE_T >::set_child_bit

(

const uint32

c)

Definition at line 91 of file suffix_trie_inl.h.

template<uint32 ALPHABET_SIZE_T, TrieType TYPE_T>

NVBIO_FORCEINLINE NVBIO_HOST_DEVICE void nvbio::TrieNode< ALPHABET_SIZE_T, TYPE_T >::set_size

(

const uint32

size)

Definition at line 99 of file suffix_trie_inl.h.

template<uint32 ALPHABET_SIZE_T, TrieType TYPE_T>

NVBIO_FORCEINLINE NVBIO_HOST_DEVICE uint32 nvbio::TrieNode< ALPHABET_SIZE_T, TYPE_T >::size

(

void

)

const

Definition at line 103 of file suffix_trie_inl.h.

Member Data Documentation

template<uint32 ALPHABET_SIZE_T, TrieType TYPE_T>

const uint32 nvbio::TrieNode< ALPHABET_SIZE_T, TYPE_T >::ALPHABET_SIZE = ALPHABET_SIZE_T

static

Definition at line 79 of file suffix_trie.h.

template<uint32 ALPHABET_SIZE_T, TrieType TYPE_T>

const uint32 nvbio::TrieNode< ALPHABET_SIZE_T, TYPE_T >::invalid_node = uint32(-1)

static

Definition at line 81 of file suffix_trie.h.

template<uint32 ALPHABET_SIZE_T, TrieType TYPE_T>

uint32 nvbio::TrieNode< ALPHABET_SIZE_T, TYPE_T >::m_child

Definition at line 119 of file suffix_trie.h.

template<uint32 ALPHABET_SIZE_T, TrieType TYPE_T>

uint32 nvbio::TrieNode< ALPHABET_SIZE_T, TYPE_T >::m_mask

Definition at line 120 of file suffix_trie.h.

template<uint32 ALPHABET_SIZE_T, TrieType TYPE_T>

uint32 nvbio::TrieNode< ALPHABET_SIZE_T, TYPE_T >::m_size

Definition at line 121 of file suffix_trie.h.

template<uint32 ALPHABET_SIZE_T, TrieType TYPE_T>

const TrieType nvbio::TrieNode< ALPHABET_SIZE_T, TYPE_T >::trie_type = TYPE_T

static

Definition at line 82 of file suffix_trie.h.

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

• E:/git/nvbio/nvbio/trie/suffix_trie.h
• E:/git/nvbio/nvbio/trie/suffix_trie_inl.h