| OpenMS 2.5.0

Classes | Namespaces | Macros | Typedefs | Functions
AhoCorasickAmbiguous.h File Reference
`#include <OpenMS/DATASTRUCTURES/SeqanIncludeWrapper.h>`
`#include <OpenMS/DATASTRUCTURES/String.h>`
`#include <OpenMS/CONCEPT/Exception.h>`
`#include <OpenMS/CONCEPT/Macros.h>`

Go to the source code of this file.

## Classes

struct | OMS_TranslateTableAAToChar_< T >
struct | OMS_TranslateTableCharToAA_< T >
struct | OMS_TranslateTableByteToAA_< T >
struct | AAcid_
struct | ValueSize< AAcid >
struct | BitsPerValue< AAcid >
struct | CompareTypeImpl< AAcid, uint8_t >
struct | CompareTypeImpl< AAcid, char >
struct | Spawn< TNeedle >
| state of an AC spawn, operating on a trie More...
struct | PatternAuxData< TNeedle >
class | Pattern< TNeedle, FuzzyAC >
struct | Host< Pattern< TNeedle, FuzzyAC > >
struct | Host< Pattern< TNeedle, FuzzyAC > const >
class | AhoCorasickAmbiguous
| Extended Aho-Corasick algorithm capable of matching ambiguous amino acids in the pattern (i.e. proteins). More...

## Namespaces

| seqan
| OpenMS
| Main OpenMS namespace.

## Macros

#define | DEBUG_ONLY if (false)

## Typedefs

typedef SimpleType< unsigned char, AAcid_ > | AAcid
typedef String< AAcid, Alloc< void > > | AAString
typedef Iterator< const AAString, Rooted >::Type | AAStringIterator
typedef Tag< FuzzyAC_ > | FuzzyAC

## Functions

AAcid | unknownValueImpl (AAcid *)
void | assign (char &c_target, AAcid const &source)
void | assign (AAcid &target, uint8_t c_source)
void | assign (AAcid &target, char c_source)
template<typename T >
void | _getSpawnRange (const AAcid c, T &idxFirst, T &idxLast)
| given an ambAA `c`, return a range of AA's (including `idxLast`) which need to be spawned. More...
template<typename TNeedle >
void | _createAcTrie (Pattern< TNeedle, FuzzyAC > &me)
template<typename TNeedle , typename TNeedle2 >
void | setHost (Pattern< TNeedle, FuzzyAC > &me, TNeedle2 const &needle)
template<typename TNeedle , typename TNeedle2 >
void | setHost (Pattern< TNeedle, FuzzyAC > &me, TNeedle2 &needle)
template<typename TNeedle >
Size< TNeedle >::Type | position (const PatternAuxData< TNeedle > &dh)
template<typename TFinder , typename TNeedle >
void | _reportHit (TFinder &finder, const Pattern< TNeedle, FuzzyAC > &me, PatternAuxData< TNeedle > &dh)
bool | isAmbiguous (AAcid c)
bool | isAmbiguous (const AAString &s)
template<typename TNeedle >
bool | _createSecondarySpawns (const Pattern< TNeedle, FuzzyAC > &me, PatternAuxData< TNeedle > &dh, Spawn< TNeedle > &spawn, const AAcid c)
template<class TNeedle >
std::string | getPath (const Pattern< TNeedle, FuzzyAC > &me, typename Pattern< TNeedle, FuzzyAC >::TVert current_state)
| for debug only More...
template<class TNeedle >
void | addHits (const Pattern< TNeedle, FuzzyAC > &me, PatternAuxData< TNeedle > &dh, const Spawn< TNeedle > &spawn)
template<class TNeedle >
void | addHits (const Pattern< TNeedle, FuzzyAC > &me, PatternAuxData< TNeedle > &dh, const typename Pattern< TNeedle, FuzzyAC >::TVert &current_state)
template<typename TNeedle >
bool | _consumeChar (const Pattern< TNeedle, FuzzyAC > &me, PatternAuxData< TNeedle > &dh, typename Pattern< TNeedle, FuzzyAC >::TVert &current, const AAcid c)
| Universal UN-ambiguous char consumer. Works for Master and Spawns. More...
template<typename TNeedle >
bool | _consumeChar (const Pattern< TNeedle, FuzzyAC > &me, PatternAuxData< TNeedle > &dh, Spawn< TNeedle > &spawn, const AAcid c)
| Consume UN-ambiguous char, while checking prefix/root conditions. More...
template<typename TNeedle >
bool | _spawnConsumeChar (const Pattern< TNeedle, FuzzyAC > &me, PatternAuxData< TNeedle > &dh, Spawn< TNeedle > &spawn, const AAcid c)
template<typename TNeedle >
void | _masterConsumeChar (const Pattern< TNeedle, FuzzyAC > &me, PatternAuxData< TNeedle > &dh, const AAcid c)
template<typename TFinder , typename TNeedle >
bool | find (TFinder &finder, const Pattern< TNeedle, FuzzyAC > &me, PatternAuxData< TNeedle > &dh)

## Class Documentation

## ◆ seqan::AAcid_

struct seqan::AAcid_

## ◆ seqan::CompareTypeImpl< AAcid, uint8_t >

struct seqan::CompareTypeImpl< AAcid, uint8_t >

### template<>
struct seqan::CompareTypeImpl< AAcid, uint8_t >

Class Members
typedef AAcid | Type |

## ◆ seqan::CompareTypeImpl< AAcid, char >

struct seqan::CompareTypeImpl< AAcid, char >

### template<>
struct seqan::CompareTypeImpl< AAcid, char >

Class Members
typedef AAcid | Type |

## ◆ seqan::Host< Pattern< TNeedle, FuzzyAC > >

struct seqan::Host< Pattern< TNeedle, FuzzyAC > >

### template<typename TNeedle>
struct seqan::Host< Pattern< TNeedle, FuzzyAC > >

Class Members
typedef TNeedle | Type |

## ◆ seqan::Host< Pattern< TNeedle, FuzzyAC > const >

struct seqan::Host< Pattern< TNeedle, FuzzyAC > const >

### template<typename TNeedle>
struct seqan::Host< Pattern< TNeedle, FuzzyAC > const >

Class Members
typedef TNeedle const | Type |

## Macro Definition Documentation

## ◆ DEBUG_ONLY

#define DEBUG_ONLY if (false)

Referenced by seqan::_createSecondarySpawns(), seqan::_masterConsumeChar(), seqan::_spawnConsumeChar(), seqan::addHits(), seqan::find(), and PeptideIndexing::run().