| OpenMS 2.5.0

Classes | Typedefs | Functions
seqan Namespace Reference

## 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 TNeedle const | 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,
|  | 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().

## ◆ _consumeChar() [2/2]

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.

## ◆ _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 | ( | char & | c_target,
|  | AAcid const & | source
| ) |  |

inline

## ◆ assign() [2/3]

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

inline

## ◆ assign() [3/3]

void seqan::assign | ( | AAcid & | target,
|  | char | c_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< UInt, std::vector< const OpenMS::ResidueModification *> >::has(), GridBasedClustering< Metric >::mergeVeto_(), InMSLevelRange< SpectrumType >::operator()(), HasPrecursorCharge< SpectrumType >::operator()(), Map< UInt, std::vector< const OpenMS::ResidueModification *> >::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 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().

## ◆ setHost() [2/2]

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

inline

References setHost().

## ◆ unknownValueImpl()

AAcid seqan::unknownValueImpl | ( | AAcid * |  | ) |

inline