ACTrieState Struct Reference

#include <OpenMS/ANALYSIS/ID/AhoCorasickAmbiguous.h>

Public Member Functions
void	setQuery (const std::string &haystack)
size_t	textPos () const
const char *	textPosIt () const
const std::string &	getQuery () const
	The current query.
AA	nextValidAA ()

Public Attributes
friend	ACScout
std::vector< Hit >	hits
std::queue< ACScout >	scouts
Index	tree_pos
	position in trie (for the Primary)

Private Attributes
const char *	it_q_ = ""
std::string	query_
	current query ( = haystack = text)

Detailed Description

A state object for an ACTrie, i.e. dynamic information when traversing the trie (which is 'const' after construction) Useful when using multi-threading; each thread can walk the trie and keep track of its state using an instance of this class

Member Function Documentation

getQuery()

const std::string & getQuery

(

)

const

The current query.

nextValidAA()

AA nextValidAA

(

)

Return the next valid AA in the query. If the query was fully traversed, an invalid AA is returned. This moves the internal iterator for the query forwards.

setQuery()

void setQuery

(

const std::string &

haystack

)

Set a haystack (query) where the needles (patterns) are to be searched This also resets the current trie-node to ROOT, and voids the hits

textPos()

size_t textPos

(

)

const

Where in the text are we currently?

Note

The result is undefined unless setQuery() was called before, since the position is computed relative to the current query (a default-constructed state points into an empty string literal instead)

textPosIt()

const char * textPosIt

(

)

const

Where in the text are we currently?

Note

See textPos(): without a preceding setQuery() this does not point into the query

Member Data Documentation

ACScout

friend ACScout

hits

std::vector<Hit> hits

current hits found

it_q_

const char* it_q_ = ""

private

position in query; defaults to an empty string literal, so that a state which never saw a setQuery() reads as 'query fully consumed' instead of dereferencing an uninitialized pointer (could happen in OpenMP context, with more threads than proteins to search, where some threads never get a protein to search)

query_

std::string query_

private

current query ( = haystack = text)

scouts

std::queue<ACScout> scouts

initial scout points which are currently active and need processing. this needs a deque: ACTrie::nextHitsNoClear_() holds a reference to front() while pushing new scouts, which only a deque (not a vector) keeps valid.

tree_pos

Index tree_pos

position in trie (for the Primary)