LocARNA-1.9.2
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Public Types | Public Member Functions
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 PatternPairSelfValuePTR
 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< SelfValuePTRpatListTYPE
 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 PatternPairgetPatternPair (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 patListTYPEgetList () const
const orderedMapTYPEgetOrderedMap () const
orderedMapTYPEgetOrderedMap2 ()
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)


Constructor & Destructor Documentation

Copy Constructor

Parameters:
myPairMapPatternPairMap

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:
idId of the PatternPair
firstfirst pattern
secondsecond pattern
structurestructure of the PatternPair
scorescore of the PatternPair

adds a PatternPair to the PatternPairMap

Parameters:
valuepointer to the PatternPair

read access

Returns:
list of PatternPairs

computes the number of mapped bases

Returns:
the number of mapped bases in the patternList

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

read access

Returns:
ordered Map

write access

Returns:
ordered Map
const PatternPair & LocARNA::PatternPairMap::getPatternPair ( const std::string &  id) const

gets the PatternPair with the Id id

Parameters:
idId of PatternPair
Returns:
PatternPair with Id id

gets the pointer to the PatternPair with the Id id

Parameters:
idId of PatternPair
Returns:
pointer to the PatternPair with Id id
const int LocARNA::PatternPairMap::size ( ) const

read access

Returns:
size of the idMap

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