seqan Namespace Reference

Classes
struct	OMS_TranslateTableAAToChar_
struct	OMS_TranslateTableCharToAA_
struct	OMS_TranslateTableByteToAA_
struct	AAcid_
struct	ValueSize< AAcid >
struct	BitsPerValue< AAcid >
struct	CompareTypeImpl< AAcid, uint8_t >
struct	CompareTypeImpl< AAcid, char >
struct	Spawn
	state of an AC spawn, operating on a trie More...
struct	PatternAuxData
class	Pattern< TNeedle, FuzzyAC >
struct	Host< Pattern< TNeedle, FuzzyAC > >
struct	Host< Pattern< TNeedle, FuzzyAC > const >

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 >

Class Members
typedef AAcid	Type

seqan::CompareTypeImpl< AAcid, char >

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

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

Referenced by shared_xerces_ptr< T >::operator=().

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< __K, _Val, _Acc, _Dist, _Cmp, _Alloc >::erase(), MessagePasserFactory< Label >::fillVectorsOfMessagePassers(), WindowMower::filterPeakSpectrumForTopNInJumpingWindow(), AhoCorasickAmbiguous::findNext(), ListUtils::getIndex(), MzTab::getOptionalColumnNames_(), ScoredProcessingResult::getScore(), Map< Key, T >::has(), OpenMS::Helpers::indexOf(), TOPPViewBase::loadFiles(), GridBasedClustering< Metric >::mergeVeto_(), InMSLevelRange< SpectrumType >::operator()(), HasPrecursorCharge< SpectrumType >::operator()(), Map< Key, T >::operator[](), TwoDOptimization::optimize(), MSNumpressCoder::NumpressConfig::setCompression(), MRMTransitionGroup< ChromatogramType, TransitionType >::subset(), and MRMTransitionGroup< ChromatogramType, TransitionType >::subsetDependent().

getPath()

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

inline

for debug only

References OpenMS::Constants::c, Pattern< TNeedle, FuzzyAC >::data_graph, and Pattern< TNeedle, FuzzyAC >::parentMap.

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(), AASequence::ConstIterator::ConstIterator(), NASequence::ConstIterator::ConstIterator(), ConstRefVector< ContainerT >::ConstRefVectorConstIterator< ValueT >::ConstRefVectorConstIterator(), DBoundingBox< D >::encloses(), DRange< D >::encloses(), AhoCorasickAmbiguous::getHitDBIndex(), AhoCorasickAmbiguous::getHitProteinPosition(), GridBasedClustering< Metric >::init_(), AASequence::Iterator::Iterator(), NASequence::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(), Peak2D::setPosition(), ChromatogramPeak::setPosition(), Peak1D::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