Pattern< TNeedle, FuzzyAC > Class Template Reference

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

Public Types
typedef uint32_t	TSize
typedef Value< TNeedle >::Type	TKeyword
typedef Value< TKeyword >::Type	TAlphabet
typedef Graph< Automaton< TAlphabet > >	TGraph
typedef VertexDescriptor< TGraph >::Type	TVert
typedef __uint8	KeyWordLengthType

Public Member Functions
	Pattern ()
void	init (TNeedle const &ndl, KeyWordLengthType max_AAA=3, KeyWordLengthType max_mm=0)
	Pattern Ctor with vector of needles, i.e. keywords/peptides. More...
	~Pattern ()

Public Attributes
const TVert	nilVal
	NULL pointer for trie; e.g. returned when no successor is found. More...
Holder< TNeedle >	data_host
	holds needles, i.e. Peptides More...
TGraph	data_graph
	regular trie data More...
String< String< TSize > >	data_map_outputNodes
	regular trie data – plus: this gets augmented with all suffix traversals which are output nodes More...
String< KeyWordLengthType >	data_node_depth
	depths of each graph node More...
KeyWordLengthType	max_ambAA
	ambiguity; default: 3 More...
KeyWordLengthType	max_mmAA
	mismatches; default: 0 More...
String< TVert >	parentMap
	allows to find parent of each node More...

Private Member Functions
	Pattern (Pattern const &other)
Pattern const &	operator= (Pattern const &other)

Member Typedef Documentation

KeyWordLengthType

typedef __uint8 KeyWordLengthType

TAlphabet

typedef Value<TKeyword>::Type TAlphabet

TGraph

typedef Graph<Automaton<TAlphabet> > TGraph

TKeyword

typedef Value<TNeedle>::Type TKeyword

TSize

typedef uint32_t TSize

TVert

typedef VertexDescriptor<TGraph>::Type TVert

Constructor & Destructor Documentation

Pattern() [1/2]

Pattern ( Pattern< TNeedle, FuzzyAC > const &  other )

private

Pattern() [2/2]

Pattern ( )

inline

~Pattern()

~Pattern ( )

inline

Member Function Documentation

init()

void init ( TNeedle const &  ndl, KeyWordLengthType  max_AAA = 3, KeyWordLengthType  max_mm = 0  )

inline

Pattern Ctor with vector of needles, i.e. keywords/peptides.

The vector ndl must not be empty!

References seqan::isAmbiguous(), and seqan::setHost().

operator=()

Pattern const& operator= ( Pattern< TNeedle, FuzzyAC > const &  other )

private

Member Data Documentation

data_graph

TGraph data_graph

regular trie data

Referenced by seqan::_consumeChar(), seqan::_createAcTrie(), seqan::_masterConsumeChar(), and seqan::setHost().

data_host

Holder<TNeedle> data_host

holds needles, i.e. Peptides

Referenced by seqan::setHost().

data_map_outputNodes

String<String<TSize> > data_map_outputNodes

regular trie data – plus: this gets augmented with all suffix traversals which are output nodes

Referenced by seqan::_createAcTrie(), seqan::addHits(), and seqan::setHost().

data_node_depth

String<KeyWordLengthType> data_node_depth

depths of each graph node

Referenced by seqan::_consumeChar(), seqan::_createAcTrie(), seqan::_masterConsumeChar(), seqan::addHits(), and seqan::find().

max_ambAA

KeyWordLengthType max_ambAA

ambiguity; default: 3

Referenced by seqan::_masterConsumeChar(), and seqan::_spawnConsumeChar().

max_mmAA

KeyWordLengthType max_mmAA

mismatches; default: 0

Referenced by seqan::_masterConsumeChar(), and seqan::_spawnConsumeChar().

nilVal

const TVert nilVal

NULL pointer for trie; e.g. returned when no successor is found.

Referenced by seqan::_consumeChar().

parentMap

String<TVert> parentMap

allows to find parent of each node

Referenced by seqan::_createAcTrie().