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

Inheritance diagram for PatternAuxData< TNeedle >:

Collaboration diagram for PatternAuxData< TNeedle >:

Public Types
typedef Size< TNeedle >::Type	TSize

typedef Value< TNeedle >::Type	TKeyword

typedef Value< TKeyword >::Type	TAlphabet

typedef Graph< Automaton< TAlphabet > >	TGraph

typedef VertexDescriptor< TGraph >::Type	TVert

typedef __uint8	KeyWordLengthType

typedef std::list< Spawn< TNeedle > >	Spawns

typedef std::list< Spawn< TNeedle > >::iterator	SpawnIt

typedef std::list< Spawn< TNeedle > >::const_iterator	SpawnCIt

Public Member Functions
	PatternAuxData ()

void	reset ()

Public Attributes
Spawns	spawns
	spawn instances currently walking the tree More...

TVert	data_lastState
	Last state of master instance in the trie. More...

String< TSize >	hits_endPositions
	All remaining keyword indices. More...

TSize	data_keywordIndex
	Current keyword that produced a hit. More...

TSize	data_needleLength
	Last length of needle to reposition finder. More...

Member Typedef Documentation

◆ KeyWordLengthType

typedef __uint8 KeyWordLengthType

◆ SpawnCIt

typedef std::list<Spawn<TNeedle> >::const_iterator SpawnCIt

◆ SpawnIt

typedef std::list<Spawn<TNeedle> >::iterator SpawnIt

◆ Spawns

typedef std::list<Spawn<TNeedle> > Spawns

◆ TAlphabet

typedef Value<TKeyword>::Type TAlphabet

◆ TGraph

typedef Graph<Automaton<TAlphabet> > TGraph

◆ TKeyword

typedef Value<TNeedle>::Type TKeyword

◆ TSize

typedef Size<TNeedle>::Type TSize

◆ TVert

typedef VertexDescriptor<TGraph>::Type TVert

Constructor & Destructor Documentation

◆ PatternAuxData()

PatternAuxData ( )

inline

Member Function Documentation

◆ reset()

void reset ( )

inline

References PatternAuxData< TNeedle >::data_keywordIndex, PatternAuxData< TNeedle >::data_lastState, PatternAuxData< TNeedle >::data_needleLength, PatternAuxData< TNeedle >::hits_endPositions, and PatternAuxData< TNeedle >::spawns.

Referenced by AhoCorasickAmbiguous::setProtein().

Member Data Documentation

◆ data_keywordIndex

TSize data_keywordIndex

Current keyword that produced a hit.

Referenced by seqan::_reportHit(), seqan::position(), and PatternAuxData< TNeedle >::reset().

◆ data_lastState

TVert data_lastState

Last state of master instance in the trie.

Referenced by seqan::_masterConsumeChar(), seqan::find(), and PatternAuxData< TNeedle >::reset().

◆ data_needleLength

TSize data_needleLength

Last length of needle to reposition finder.

Referenced by seqan::_reportHit(), seqan::find(), and PatternAuxData< TNeedle >::reset().

◆ hits_endPositions

String<TSize> hits_endPositions

All remaining keyword indices.

Referenced by seqan::_reportHit(), seqan::addHits(), seqan::find(), and PatternAuxData< TNeedle >::reset().

◆ spawns

Spawns spawns

spawn instances currently walking the tree

Referenced by seqan::_createSecondarySpawns(), seqan::_masterConsumeChar(), seqan::_spawnConsumeChar(), seqan::find(), and PatternAuxData< TNeedle >::reset().

Public Types

Public Member Functions

Public Attributes