LocARNA::PatternPairMap Class Reference

manage a set of EPMs (PatternPair) More...

#include <exact_matcher.hh>

Public Types
typedef PatternPair	selfValueTYPE
	PatternPair.
typedef PatternPair *	SelfValuePTR
	pointer to PatternPair
typedef std::multimap< int, SelfValuePTR, std::greater< int > >	orderedMapTYPE
	ordered map type
typedef orderedMapTYPE::const_iterator	orderedMapCITER
	const iterator for the map
typedef orderedMapTYPE::iterator	orderedMapITER
	iterator for the map
typedef std::vector< std::unique_ptr< selfValueTYPE > >	patListTYPE
	list of patternPairs
typedef patListTYPE::iterator	patListITER
	iterator for the list of PatternPairs
typedef patListTYPE::const_iterator	patListCITER
	const iterator for the list of PatternPairs
typedef std::unordered_map< std::string, SelfValuePTR >	PatternIdMapTYPE
	map type patternId -> pointer to PatternPair

Public Member Functions
	PatternPairMap ()
	Contructor.
	PatternPairMap (const PatternPairMap &myPairMap)=delete
virtual	~PatternPairMap ()
	Destructor.
void	add (const std::string &id, const SinglePattern &first, const SinglePattern &second, const std::string &structure, int score)
	adds a PatternPair consisting of two SinglePatterns to the PatternPairMap More...
void	add (const SelfValuePTR value)
	adds a PatternPair to the PatternPairMap More...
void	makeOrderedMap ()
	creates the ordered Map
const PatternPair &	getPatternPair (const std::string &id) const
	gets the PatternPair with the Id id More...
const SelfValuePTR	getPatternPairPTR (const std::string &id) const
	gets the pointer to the PatternPair with the Id id More...
const patListTYPE &	getList () const
const orderedMapTYPE &	getOrderedMap () const
orderedMapTYPE &	getOrderedMap2 ()
const int	size () const
int	getMapBases ()
	computes the number of mapped bases More...
int	getMapEPMScore ()
	computes the score of the list of PatternPairs patternList More...
const int	getMinPatternSize () const

Detailed Description

manage a set of EPMs (PatternPair)

Member Function Documentation

add() [1/2]

void LocARNA::PatternPairMap::add

(

const SelfValuePTR

value

)

adds a PatternPair to the PatternPairMap

Parameters

value

pointer to the PatternPair

add() [2/2]

void LocARNA::PatternPairMap::add	(	const std::string &	id,
		const SinglePattern &	first,
		const SinglePattern &	second,
		const std::string &	structure,
		int	score
	)

adds a PatternPair consisting of two SinglePatterns to the PatternPairMap

Parameters

id	Id of the PatternPair
first	first pattern
second	second pattern
structure	structure of the PatternPair
score	score of the PatternPair

getList()

const PatternPairMap::patListTYPE & LocARNA::PatternPairMap::getList

(

)

const

read access

Returns

list of PatternPairs

getMapBases()

int LocARNA::PatternPairMap::getMapBases

(

)

computes the number of mapped bases

Returns

the number of mapped bases in the patternList

getMapEPMScore()

int LocARNA::PatternPairMap::getMapEPMScore

(

)

computes the score of the list of PatternPairs patternList

Returns

the sum of scores of all EPMs in the patternList

getMinPatternSize()

const int LocARNA::PatternPairMap::getMinPatternSize ( ) const

inline

read access

Returns

the minimum size of a Pattern

getOrderedMap()

const PatternPairMap::orderedMapTYPE & LocARNA::PatternPairMap::getOrderedMap

(

)

const

read access

Returns

ordered Map

getOrderedMap2()

PatternPairMap::orderedMapTYPE & LocARNA::PatternPairMap::getOrderedMap2

(

)

write access

Returns

ordered Map

getPatternPair()

const PatternPair & LocARNA::PatternPairMap::getPatternPair

(

const std::string &

id

)

const

gets the PatternPair with the Id id

Parameters

id	Id of PatternPair

Returns

PatternPair with Id id

getPatternPairPTR()

const PatternPairMap::SelfValuePTR LocARNA::PatternPairMap::getPatternPairPTR

(

const std::string &

id

)

const

gets the pointer to the PatternPair with the Id id

Parameters

id	Id of PatternPair

Returns

pointer to the PatternPair with Id id

size()

const int LocARNA::PatternPairMap::size

(

)

const

read access

Returns

size of the idMap

---

The documentation for this class was generated from the following files:

• src/LocARNA/exact_matcher.hh
• src/LocARNA/exact_matcher.cc