A class that contains information for a single Kmer.

#include <kmerClass.h>

Public Member Functions
	KmerClass (std::string kmer)

virtual	~KmerClass ()
	Class Destructor.

Getters
Constant functions to return properties of the Kmer
const std::string &	getKmer () const

const std::bitset< 8 > &	getKFlags () const

const std::set< long long > &	getKPositions () const

const std::set< ft::ReadID > &	getReadIDs () const

uint	getOCC () const

Setters
Non-constant functions to update properties of the kmer class
void	setKFlags (std::set< ft::FlagType > kFlags)

void	setKPositions (const std::set< long long > &kPositions)

void	adjustPosForOffset (uint offset=0)

void	setReadIDs (std::set< ft::ReadID > readIDs)

void	setOCC (uint occ)

Adders
Non-constant functions to add properties to the kmer class
void	addKFlag (const ft::FlagType &kFlag)

void	addKPosition (const size_t &kPosition, const uint &offset=0)

void	addReadID (const ft::ReadID &readID)

Removers
Non-constant functions to remove properties from the kmer class
void	removeKFlag (ft::FlagType kFlag)

void	removeKPosition (size_t kPosition, uint offset=0)

void	removeReadID (ft::ReadID readID)

Checkers
Constant functions to check the properties of the kmer class
bool	isKmerEqual (const KmerClass &test) const

bool	hasKmer (const std::string &test) const

bool	hasFlag (const ft::FlagType &flag)

bool	hasKPosition (const size_t &position) const

bool	hasReadID (const ft::ReadID &readID) const

Manipulation
Functions to convert between index positions, and read IDs
void	convertPosToReadID (uint readLength, uint numOfReads, bool pairedReads, bool indexRevComp=false)

bool	matchingReadID (const ft::ReadID &a, const ft::ReadID &b) const

void	adjustPositionsWithOffset (uint offset)

Overloaded Operators
bool	operator< (const ft::KmerClass &k) const

bool	operator== (const ft::KmerClass &k) const

Private Attributes
Properties
std::string	_kmer

std::bitset< 8 >	_kFlags

std::set< long long >	_positions

std::set< ft::ReadID >	_readIDs

uint	_occ

bool	_isOffsetAdjusted

Constructor & Destructor Documentation

◆ KmerClass()

ft::KmerClass::KmerClass ( std::string kmer )

Constructor

Parameters

string Kmer

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

flextyper/includes/kmerClass.h
flextyper/src/kmerClass.cpp

Public Member Functions

Private Attributes

Constructor & Destructor Documentation

◆ KmerClass()