OpenMS  2.8.0
Public Member Functions | Public Attributes | List of all members
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:
[legend]

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