Classes
struct	AAcid_

struct	AdaptedIdentity

struct	BitsPerValue< AAcid >

struct	CompareTypeImpl< AAcid, char >

struct	CompareTypeImpl< AAcid, uint8_t >

struct	Host< Pattern< TNeedle, FuzzyAC > >

struct	Host< Pattern< TNeedle, FuzzyAC > const >

struct	OMS_TranslateTableAAToChar_

struct	OMS_TranslateTableByteToAA_

struct	OMS_TranslateTableCharToAA_

struct	PAM30MS

class	Pattern< TNeedle, FuzzyAC >

struct	PatternAuxData

struct	ScoringMatrixData_< int, AminoAcid, AdaptedIdentity >

struct	ScoringMatrixData_< int, AminoAcid, PAM30MS >

struct	Spawn
	state of an AC spawn, operating on a trie More...

struct	ValueSize< AAcid >

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::AdaptedIdentity

struct seqan::AdaptedIdentity

◆ seqan::CompareTypeImpl< AAcid, char >

struct seqan::CompareTypeImpl< AAcid, char >

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

Class Members
typedef AAcid	Type

◆ seqan::CompareTypeImpl< AAcid, uint8_t >

struct seqan::CompareTypeImpl< AAcid, uint8_t >

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

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

◆ seqan::PAM30MS

struct seqan::PAM30MS

Typedef Documentation

◆ AAcid

typedef SimpleType<unsigned char, AAcid_> AAcid

◆ AAString

typedef String<AAcid, Alloc<void> > AAString

◆ AAStringIterator

typedef Iterator<const AAString, Rooted>::Type AAStringIterator

◆ FuzzyAC

typedef Tag<FuzzyAC_> FuzzyAC

Function Documentation

◆ _consumeChar() [1/2]

bool seqan::_consumeChar	(	const Pattern< TNeedle, FuzzyAC > &	me,
		PatternAuxData< TNeedle > &	dh,
		Spawn< TNeedle > &	spawn,
		const AAcid	c
	)

inline

Consume UN-ambiguous char, while checking prefix/root conditions.

Adds hits to dh and updates spawn.current_state and spawn.max_depth_decrease

Return false if new state is root, true otherwise.

References addHits(), OpenMS::Constants::c, Spawn< TNeedle >::current_state, Pattern< TNeedle, FuzzyAC >::data_graph, Pattern< TNeedle, FuzzyAC >::data_node_depth, Spawn< TNeedle >::max_depth_decrease, and Pattern< TNeedle, FuzzyAC >::nilVal.

◆ _consumeChar() [2/2]

bool seqan::_consumeChar	(	const Pattern< TNeedle, FuzzyAC > &	me,
		PatternAuxData< TNeedle > &	dh,
		typename Pattern< TNeedle, FuzzyAC >::TVert &	current,
		const AAcid	c
	)

inline

Universal UN-ambiguous char consumer. Works for Master and Spawns.

Updates current by consuming the char. Adds hits to dh after settling.

Returns: False if it reached the 'root', true otherwise

References addHits(), OpenMS::Constants::c, Pattern< TNeedle, FuzzyAC >::data_graph, and Pattern< TNeedle, FuzzyAC >::nilVal.

Referenced by _createSecondarySpawns(), _masterConsumeChar(), and _spawnConsumeChar().

◆ _createAcTrie()

void seqan::_createAcTrie ( Pattern< TNeedle, FuzzyAC > & me )

inline

< allows to find parent of each node

< allows to find character that led us to current node

< allows to find parent of each node

< trie suffix links (temporary only)

< node depths

< range of unambiguous AAcids: AAcid(idx)

create failure function (suffix links) and output function

References _getSpawnRange(), Pattern< TNeedle, FuzzyAC >::data_graph, Pattern< TNeedle, FuzzyAC >::data_map_outputNodes, Pattern< TNeedle, FuzzyAC >::data_node_depth, and Pattern< TNeedle, FuzzyAC >::parentMap.

Referenced by setHost().

◆ _createSecondarySpawns()

bool seqan::_createSecondarySpawns	(	const Pattern< TNeedle, FuzzyAC > &	me,
		PatternAuxData< TNeedle > &	dh,
		Spawn< TNeedle > &	spawn,
		const AAcid	c
	)

inline

References _consumeChar(), _getSpawnRange(), Spawn< TNeedle >::ambAA_seen, OpenMS::Constants::c, Spawn< TNeedle >::current_state, DEBUG_ONLY, getPath(), isAmbiguous(), Spawn< TNeedle >::max_depth_decrease, and PatternAuxData< TNeedle >::spawns.

◆ _getSpawnRange()

void seqan::_getSpawnRange	(	const AAcid	c,
		T &	idxFirst,
		T &	idxLast
	)

inline

given an ambAA c, return a range of AA's (including idxLast) which need to be spawned.

The range can be converted to AAcids via 'AAcid(T)'.

References OpenMS::Constants::c.

Referenced by _createAcTrie(), _createSecondarySpawns(), _masterConsumeChar(), and _spawnConsumeChar().

◆ _masterConsumeChar()

void seqan::_masterConsumeChar	(	const Pattern< TNeedle, FuzzyAC > &	me,
		PatternAuxData< TNeedle > &	dh,
		const AAcid	c
	)

inline

References _consumeChar(), _getSpawnRange(), OpenMS::Constants::c, Pattern< TNeedle, FuzzyAC >::data_graph, PatternAuxData< TNeedle >::data_lastState, Pattern< TNeedle, FuzzyAC >::data_node_depth, DEBUG_ONLY, isAmbiguous(), Pattern< TNeedle, FuzzyAC >::max_ambAA, Pattern< TNeedle, FuzzyAC >::max_mmAA, and PatternAuxData< TNeedle >::spawns.

Referenced by find().

◆ _reportHit()

void seqan::_reportHit	(	TFinder &	finder,
		const Pattern< TNeedle, FuzzyAC > &	me,
		PatternAuxData< TNeedle > &	dh
	)

inline

References PatternAuxData< TNeedle >::data_keywordIndex, PatternAuxData< TNeedle >::data_needleLength, PatternAuxData< TNeedle >::hits_endPositions, and position().

Referenced by find().

◆ _spawnConsumeChar()

bool seqan::_spawnConsumeChar	(	const Pattern< TNeedle, FuzzyAC > &	me,
		PatternAuxData< TNeedle > &	dh,
		Spawn< TNeedle > &	spawn,
		const AAcid	c
	)

inline

References _consumeChar(), _getSpawnRange(), Spawn< TNeedle >::ambAA_seen, OpenMS::Constants::c, Spawn< TNeedle >::current_state, DEBUG_ONLY, getPath(), isAmbiguous(), Pattern< TNeedle, FuzzyAC >::max_ambAA, Spawn< TNeedle >::max_depth_decrease, Pattern< TNeedle, FuzzyAC >::max_mmAA, Spawn< TNeedle >::mismatches_seen, and PatternAuxData< TNeedle >::spawns.

Referenced by find().

◆ addHits() [1/2]

void seqan::addHits	(	const Pattern< TNeedle, FuzzyAC > &	me,
		PatternAuxData< TNeedle > &	dh,
		const Spawn< TNeedle > &	spawn
	)

inline

References OpenMS::StringConversions::append(), Spawn< TNeedle >::current_state, Pattern< TNeedle, FuzzyAC >::data_map_outputNodes, Pattern< TNeedle, FuzzyAC >::data_node_depth, DEBUG_ONLY, PatternAuxData< TNeedle >::hits_endPositions, and Spawn< TNeedle >::max_depth_decrease.

Referenced by _consumeChar().

◆ addHits() [2/2]

void seqan::addHits	(	const Pattern< TNeedle, FuzzyAC > &	me,
		PatternAuxData< TNeedle > &	dh,
		const typename Pattern< TNeedle, FuzzyAC >::TVert &	current_state
	)

inline

References OpenMS::StringConversions::append(), Pattern< TNeedle, FuzzyAC >::data_map_outputNodes, DEBUG_ONLY, and PatternAuxData< TNeedle >::hits_endPositions.

◆ assign() [1/3]

void seqan::assign	(	AAcid &	target,
		char	c_source
	)

inline

◆ assign() [2/3]

void seqan::assign	(	AAcid &	target,
		uint8_t	c_source
	)

inline

◆ assign() [3/3]

void seqan::assign	(	char &	c_target,
		AAcid const &	source
	)

inline

◆ find()

bool seqan::find	(	TFinder &	finder,
		const Pattern< TNeedle, FuzzyAC > &	me,
		PatternAuxData< TNeedle > &	dh
	)

inline

References _masterConsumeChar(), _reportHit(), _spawnConsumeChar(), OpenMS::Constants::c, PatternAuxData< TNeedle >::data_lastState, PatternAuxData< TNeedle >::data_needleLength, Pattern< TNeedle, FuzzyAC >::data_node_depth, DEBUG_ONLY, getPath(), PatternAuxData< TNeedle >::hits_endPositions, and PatternAuxData< TNeedle >::spawns.

Referenced by ScoredProcessingResult::addProcessingStep(), ListUtils::contains(), XMLHandler::cvStringToEnum_(), KDTree< 2, KDTreeFeatureNode >::erase(), MessagePasserFactory< Label >::fillVectorsOfMessagePassers(), WindowMower::filterPeakSpectrumForTopNInJumpingWindow(), AhoCorasickAmbiguous::findNext(), ListUtils::getIndex(), MzTab::getOptionalColumnNames_(), ScoredProcessingResult::getScore(), Map< char, double >::has(), OpenMS::Helpers::indexOf(), GridBasedClustering< Metric >::mergeVeto_(), InMSLevelRange< SpectrumType >::operator()(), HasPrecursorCharge< SpectrumType >::operator()(), Map< char, double >::operator[](), TwoDOptimization::optimize(), MSNumpressCoder::NumpressConfig::setCompression(), MRMTransitionGroup< SpectrumT, TransitionT >::subset(), and MRMTransitionGroup< SpectrumT, TransitionT >::subsetDependent().

◆ getPath()

std::string seqan::getPath	(	const Pattern< TNeedle, FuzzyAC > &	me,
		typename Pattern< TNeedle, FuzzyAC >::TVert	current_state
	)

inline

for debug only

Referenced by _createSecondarySpawns(), _spawnConsumeChar(), and find().

◆ isAmbiguous() [1/2]

bool seqan::isAmbiguous ( AAcid c )

inline

References OpenMS::Constants::c.

Referenced by _createSecondarySpawns(), _masterConsumeChar(), _spawnConsumeChar(), Pattern< TNeedle, FuzzyAC >::init(), isAmbiguous(), and PeptideIndexing::run().

◆ isAmbiguous() [2/2]

bool seqan::isAmbiguous ( const AAString & s )

inline

References isAmbiguous().

◆ position()

Size<TNeedle>::Type seqan::position ( const PatternAuxData< TNeedle > & dh )

inline

References PatternAuxData< TNeedle >::data_keywordIndex.

Referenced by _reportHit(), AveragePosition< D >::add(), PeptideIndexing::FoundProteinFunctor::addHit(), NASequence::ConstIterator::ConstIterator(), AASequence::ConstIterator::ConstIterator(), ConstRefVector< ContainerT >::ConstRefVectorConstIterator< ValueT >::ConstRefVectorConstIterator(), DBoundingBox< 2 >::encloses(), DRange< 3 >::encloses(), AhoCorasickAmbiguous::getHitDBIndex(), AhoCorasickAmbiguous::getHitProteinPosition(), GridBasedClustering< Metric >::init_(), NASequence::Iterator::Iterator(), AASequence::Iterator::Iterator(), OpenMS::operator*(), OpenMS::operator/(), EnzymaticDigestionLogModel::BindingSite_::operator<(), DeNovoIonScoring::IonScore::operator=(), EnzymaticDigestionLogModel::BindingSite_::operator==(), MultiGradient::precalculatedColorAt(), MultiGradient::precalculatedColorIndex(), DIntervalBase< D >::setMax(), DIntervalBase< D >::setMin(), Peak1D::setPosition(), ChromatogramPeak::setPosition(), Peak2D::setPosition(), and PeptideIndexing::PeptideProteinMatchInformation::tie().

◆ setHost() [1/2]

void seqan::setHost	(	Pattern< TNeedle, FuzzyAC > &	me,
		TNeedle2 &	needle
	)

inline

References setHost().

◆ setHost() [2/2]

void seqan::setHost	(	Pattern< TNeedle, FuzzyAC > &	me,
		TNeedle2 const &	needle
	)

References _createAcTrie(), Pattern< TNeedle, FuzzyAC >::data_graph, Pattern< TNeedle, FuzzyAC >::data_host, and Pattern< TNeedle, FuzzyAC >::data_map_outputNodes.

Referenced by Pattern< TNeedle, FuzzyAC >::init(), and setHost().

◆ unknownValueImpl()

AAcid seqan::unknownValueImpl ( AAcid * )

inline

Classes

Typedefs

Functions

Class Documentation

◆ seqan::AAcid_

◆ seqan::AdaptedIdentity

◆ seqan::CompareTypeImpl< AAcid, char >

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

◆ seqan::CompareTypeImpl< AAcid, uint8_t >

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

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

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

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

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

◆ seqan::PAM30MS

Typedef Documentation

◆ AAcid

◆ AAString

◆ AAStringIterator

◆ FuzzyAC

Function Documentation

◆ _consumeChar() [1/2]

◆ _consumeChar() [2/2]

◆ _createAcTrie()

◆ _createSecondarySpawns()

◆ _getSpawnRange()

◆ _masterConsumeChar()

◆ _reportHit()

◆ _spawnConsumeChar()

◆ addHits() [1/2]

◆ addHits() [2/2]

◆ assign() [1/3]

◆ assign() [2/3]

◆ assign() [3/3]

◆ find()

◆ getPath()

◆ isAmbiguous() [1/2]

◆ isAmbiguous() [2/2]

◆ position()

◆ setHost() [1/2]

◆ setHost() [2/2]

◆ unknownValueImpl()

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

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

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

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