nvbio::SortedDictionarySuffixTrie< ALPHABET_SIZE_T, Iterator > Struct Template Reference

Detailed description

template< uint32 ALPHABET_SIZE_T, typename Iterator>
struct nvbio::SortedDictionarySuffixTrie< ALPHABET_SIZE_T, Iterator >

A suffix trie type built on a generic dictionary of sorted strings

Template Parameters

ALPHABET_SIZE_T	the size of the alphabet
Iterator	an iterator to the sorted string dictionary

Definition at line 65 of file sorted_dictionary.h.

#include <sorted_dictionary.h>

Public Types
typedef std::iterator_traits < Iterator >::value_type	string_type
typedef SortedDictionaryNode	node_type

Public Methods
NVBIO_FORCEINLINE NVBIO_HOST_DEVICE	SortedDictionarySuffixTrie (const Iterator seq, const uint32 size)
NVBIO_FORCEINLINE NVBIO_HOST_DEVICE node_type	root () const
template<typename Visitor >
NVBIO_FORCEINLINE NVBIO_HOST_DEVICE void	children (const node_type node, Visitor &visitor) const
NVBIO_FORCEINLINE NVBIO_HOST_DEVICE bool	is_leaf (const node_type node) const
NVBIO_FORCEINLINE NVBIO_HOST_DEVICE uint32	size (const node_type node) const

Static Public Members
static const uint32	ALPHABET_SIZE = ALPHABET_SIZE_T

Member Typedef Documentation

template<uint32 ALPHABET_SIZE_T, typename Iterator >

typedef SortedDictionaryNode nvbio::SortedDictionarySuffixTrie< ALPHABET_SIZE_T, Iterator >::node_type

Definition at line 70 of file sorted_dictionary.h.

template<uint32 ALPHABET_SIZE_T, typename Iterator >

typedef std::iterator_traits<Iterator>::value_type nvbio::SortedDictionarySuffixTrie< ALPHABET_SIZE_T, Iterator >::string_type

Definition at line 69 of file sorted_dictionary.h.

Constructor & Destructor Documentation

template<uint32 ALPHABET_SIZE_T, typename Iterator >

NVBIO_FORCEINLINE NVBIO_HOST_DEVICE nvbio::SortedDictionarySuffixTrie< ALPHABET_SIZE_T, Iterator >::SortedDictionarySuffixTrie	(	const Iterator	seq,
		const uint32	size
	)

constructor

Definition at line 40 of file sorted_dictionary_inl.h.

Member Function Documentation

template<uint32 ALPHABET_SIZE_T, typename Iterator >

template<typename Visitor >

NVBIO_FORCEINLINE NVBIO_HOST_DEVICE void nvbio::SortedDictionarySuffixTrie< ALPHABET_SIZE_T, Iterator >::children	(	const node_type	node,
		Visitor &	visitor
	)		const

visit the children of a given node

Template Parameters

Visitor

a visitor implementing the following interface: struct Visitor { // do something with the node corresponding to character c void visit(const uint8 c, const NodeType node); }

Definition at line 59 of file sorted_dictionary_inl.h.

template<uint32 ALPHABET_SIZE_T, typename Iterator >

NVBIO_FORCEINLINE NVBIO_HOST_DEVICE bool nvbio::SortedDictionarySuffixTrie< ALPHABET_SIZE_T, Iterator >::is_leaf

(

const node_type

node)

const

return true if the node is a leaf

Definition at line 87 of file sorted_dictionary_inl.h.

template<uint32 ALPHABET_SIZE_T, typename Iterator >

NVBIO_FORCEINLINE NVBIO_HOST_DEVICE SortedDictionarySuffixTrie< ALPHABET_SIZE_T, Iterator >::node_type nvbio::SortedDictionarySuffixTrie< ALPHABET_SIZE_T, Iterator >::root

(

)

const

return the root node of the dictionary seen as a trie

Definition at line 49 of file sorted_dictionary_inl.h.

template<uint32 ALPHABET_SIZE_T, typename Iterator >

NVBIO_FORCEINLINE NVBIO_HOST_DEVICE uint32 nvbio::SortedDictionarySuffixTrie< ALPHABET_SIZE_T, Iterator >::size

(

const node_type

node)

const

return the size of a node

Definition at line 96 of file sorted_dictionary_inl.h.

Member Data Documentation

template<uint32 ALPHABET_SIZE_T, typename Iterator >

const uint32 nvbio::SortedDictionarySuffixTrie< ALPHABET_SIZE_T, Iterator >::ALPHABET_SIZE = ALPHABET_SIZE_T

static

Definition at line 67 of file sorted_dictionary.h.

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

• E:/git/nvbio/nvbio/trie/sorted_dictionary.h
• E:/git/nvbio/nvbio/trie/sorted_dictionary_inl.h