OpenMS  2.6.0
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 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

◆ _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

◆ _reportHit()

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

◆ _spawnConsumeChar()

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

◆ addHits() [1/2]

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

◆ addHits() [2/2]

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

◆ 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

◆ 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

◆ isAmbiguous() [2/2]

bool seqan::isAmbiguous ( const AAString s)
inline

References isAmbiguous().

◆ position()

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

◆ 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 
)

◆ unknownValueImpl()

AAcid seqan::unknownValueImpl ( AAcid )
inline