| OpenMS 2.5.0

Public Types | Public Member Functions | Public Attributes | Private Member Functions | List of all members
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().