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::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 |
manage a set of EPMs (PatternPair)
LocARNA::PatternPairMap::PatternPairMap | ( | const PatternPairMap & | myPairMap | ) | [inline] |
Copy Constructor
myPairMap | PatternPairMap |
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
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
value | pointer to the PatternPair |
const PatternPairMap::patListTYPE & LocARNA::PatternPairMap::getList | ( | ) | const |
read access
computes the number of mapped bases
computes the score of the list of PatternPairs patternList
const int LocARNA::PatternPairMap::getMinPatternSize | ( | ) | const [inline] |
read access
const PatternPairMap::orderedMapTYPE & LocARNA::PatternPairMap::getOrderedMap | ( | ) | const |
read access
write access
const PatternPair & LocARNA::PatternPairMap::getPatternPair | ( | const std::string & | id | ) | const |
const PatternPairMap::SelfValuePTR LocARNA::PatternPairMap::getPatternPairPTR | ( | const std::string & | id | ) | const |
gets the pointer to the PatternPair with the Id id
id | Id of PatternPair |
const int LocARNA::PatternPairMap::size | ( | ) | const |
read access