LocARNA::PatternPairMap Class Reference

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

#include <exact_matcher.hh>

List of all members.

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::list< SelfValuePTR >	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 unordered_map < std::string, SelfValuePTR > ::type	PatternIdMapTYPE
	map type patternId -> pointer to PatternPair
Public Member Functions
	PatternPairMap ()
	Contructor.
	PatternPairMap (const PatternPairMap &myPairMap)
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
void	add (const SelfValuePTR value)
	adds a PatternPair to the PatternPairMap
void	makeOrderedMap ()
	creates the ordered Map
void	updateFromMap ()
	updates the PatternPairMap from the ordered Map
const PatternPair &	getPatternPair (const std::string &id) const
	gets the PatternPair with the Id id
const SelfValuePTR	getPatternPairPTR (const std::string &id) const
	gets the pointer to the PatternPair with the Id id
const patListTYPE &	getList () const
const orderedMapTYPE &	getOrderedMap () const
orderedMapTYPE &	getOrderedMap2 ()
const int	size () const
int	getMapBases ()
	computes the number of mapped bases
int	getMapEPMScore ()
	computes the score of the list of PatternPairs patternList
const int	getMinPatternSize () const

---

Detailed Description

manage a set of EPMs (PatternPair)

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Constructor & Destructor Documentation

LocARNA::PatternPairMap::PatternPairMap

(

const PatternPairMap &

myPairMap

)

[inline]

Copy Constructor

Parameters:

myPairMap

PatternPairMap

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Member Function Documentation

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

void LocARNA::PatternPairMap::add

(

const SelfValuePTR

value

)

adds a PatternPair to the PatternPairMap

Parameters:

value

pointer to the PatternPair

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

(

)

const

read access

Returns:

list of PatternPairs

int LocARNA::PatternPairMap::getMapBases

(

)

computes the number of mapped bases

Returns:

the number of mapped bases in the patternList

int LocARNA::PatternPairMap::getMapEPMScore

(

)

computes the score of the list of PatternPairs patternList

Returns:

the sum of scores of all EPMs in the patternList

const int LocARNA::PatternPairMap::getMinPatternSize

(

)

const [inline]

read access

Returns:

the minimum size of a Pattern

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

(

)

const

read access

Returns:

ordered Map

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

(

)

write access

Returns:

ordered Map

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

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

const int LocARNA::PatternPairMap::size

(

)

const

read access

Returns:

size of the idMap

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

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