AhoCorasickAmbiguous.h File Reference

#include <OpenMS/DATASTRUCTURES/SeqanIncludeWrapper.h>
#include <OpenMS/DATASTRUCTURES/String.h>
#include <OpenMS/CONCEPT/Exception.h>
#include <OpenMS/CONCEPT/Macros.h>

Include dependency graph for AhoCorasickAmbiguous.h:

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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)

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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 const TNeedle	Type

Macro Definition Documentation

DEBUG_ONLY

#define DEBUG_ONLY   if (false)