A class that contains information for the FlexTyper Instance.

#include <ftMapClass.h>

Public Member Functions
	FTMap (const FTProp &_ftProps)

virtual	~FTMap ()
	Class Destructor.

init
Functions to set up the FTMap
void	addInputQueries (const std::set< Query > &inputQueries)

void	genQKMap ()

Getters
Constant functions to return properties of the query
const std::vector< std::map< std::string, ft::KmerClass > > &	getResults ()

const FTProp &	getFTProps () const

const std::unordered_map< std::string, ft::KmerClass > &	getKmerSet () const

Access
Access functions for single kmer and queries
bool	checkForKmer (const std::string &testKmer) const

void	addKmer (const std::string &kmer)

const ft::KmerClass &	getKmer (const std::string &kmer) const

bool	checkForQIDT (const ft::QIdT &testQueryObject) const

void	addQuery (int queryID, ft::QueryType queryType, const std::string &queryString)

const ft::QueryClass &	getQuery (const ft::QIdT &qIDT) const

void	addReadIDsToQuery (ft::QIdT qIDT, std::set< ft::ReadID > &readIds)

Results
Functions to process the results of a search
void	addIndexResults (const std::map< std::string, ft::KmerClass > &indexResults)

void	addKmerResults (const ft::KmerClass &kmerResult)

void	processResults ()

void	processIndexResults (const std::map< std::string, ft::KmerClass > &indexResults)

void	processQueryResults (const ft::QIdT &qIDT)

void	addKmersToQueryResults (ft::QueryClass &query, std::set< std::string > &kmers, std::set< ft::ReadID > &readIds)

int	calculateQueryCount (const std::set< ft::ReadID > &readIds)

void	removeMultiHits ()

void	removeMultiHitsAsPairs ()

Private Attributes
Properties
FTProp	_ftProps

std::unordered_map< std::string, ft::KmerClass >	_kmerSet

std::map< ft::QIdT, ft::QueryClass >	_querySet

QKMap	_qkMap

QKMap	_qkRCMap

std::vector< std::map< std::string, ft::KmerClass > >	_searchResults

Constructor & Destructor Documentation

◆ FTMap()

ft::FTMap::FTMap ( const FTProp & _ftProps )

Constructor

Parameters

FTProp FlexTyper Properties for this instance

Member Function Documentation

◆ removeMultiHits()

void ft::FTMap::removeMultiHits ( )

< bool = whether its added to adjustment (gets added when its seen for the second time)

query to adjust, amount to adjust count by

iterate through and compile a list of multihits

if read hasnt been observed

add to observed Reads

add to new reads

if query isnt marked for adjustment

add to list of queries to adjust

< iterate through and remove multi hit reads, adjust query counts

◆ removeMultiHitsAsPairs()

void ft::FTMap::removeMultiHitsAsPairs ( )

< int = Read ID (ignoring pair)