ACSpawn Struct Reference

a spin-off search path through the trie, which can deal with ambiguous AAs and mismatches More...

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

Collaboration diagram for ACSpawn:

Public Member Functions
	ACSpawn ()=delete
	No default C'tor. More...
	ACSpawn (std::string::const_iterator query_pos, Index tree_pos, uint8_t max_aa, uint8_t max_mm, uint8_t max_prefix_loss)
	C'tor with arguments. More...
size_t	textPos (const ACTrieState &state) const
	Where in the text are we currently? More...
AA	nextValidAA (const ACTrieState &state)

Public Attributes
std::string::const_iterator	it_query
	position in query More...
Index	tree_pos
	position in trie More...
uint8_t	max_aaa_leftover {0}
	number of ambiguous AAs the spawn can yet tolerate before exceeding the limit More...
uint8_t	max_mm_leftover {0}
	number of mismatches the spawn can yet tolerate before exceeding the limit More...
uint8_t	max_prefix_loss_leftover {0}
	number of AA's which can get lost by following suffix links, before the spawn must retire; reaching 0 means retire More...

Detailed Description

a spin-off search path through the trie, which can deal with ambiguous AAs and mismatches

Constructor & Destructor Documentation

ACSpawn() [1/2]

ACSpawn ( )

delete

No default C'tor.

ACSpawn() [2/2]

ACSpawn	(	std::string::const_iterator	query_pos,
		Index	tree_pos,
		uint8_t	max_aa,
		uint8_t	max_mm,
		uint8_t	max_prefix_loss
	)

C'tor with arguments.

Member Function Documentation

nextValidAA()

AA nextValidAA

(

const ACTrieState &

state

)

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.

textPos()

size_t textPos

(

const ACTrieState &

state

)

const

Where in the text are we currently?

Member Data Documentation

it_query

std::string::const_iterator it_query

position in query

max_aaa_leftover

uint8_t max_aaa_leftover {0}

number of ambiguous AAs the spawn can yet tolerate before exceeding the limit

max_mm_leftover

uint8_t max_mm_leftover {0}

number of mismatches the spawn can yet tolerate before exceeding the limit

max_prefix_loss_leftover

uint8_t max_prefix_loss_leftover {0}

number of AA's which can get lost by following suffix links, before the spawn must retire; reaching 0 means retire

tree_pos

Index tree_pos

position in trie