FTSearch¶

namespace ft¶

FILE ikmergenerator.h

DESCRIPTION This file contains the declaration of kmergenerator interface

class FTSearch¶

#include <ftsearch.h>

This file contains the definition of ftsearch. The class can be summarized as the init point for the application. The init function calls other parts of the application.

Copyright: Copyright (c) 2019, Wasserman lab
Author: Godfrain Jacques Kounkou

Public Functions

FTSearch::FTSearch()¶: FTSearch.

ft::FTSearch::~FTSearch()¶: ~FTSearch

void FTSearch::init(const fs::path & pathToQueryFile, uint kmerSize, uint readLength, const fs::path & indexLocation, const fs::path & outputFile, bool refOnly, SearchType searchType, bool multithread = false, const fs::path & inputFastQ = ”“, uint overlap = 0, bool returnMatchesOnly = false, bool kmerCounts = false, uint stride = 10, uint maxOccurences = 200, uint threadNumber = 1, bool ignoreNonUniqueKmers = true, bool crossover = false, bool printSearchTime = false, uint maxKmers = UINT_MAX, uint totalKmers = UINT_MAX, const fs::path & matchingReads = ”“)¶

search

Parameters

pathToQueryFile:
kmerSize:
readLength:
listIndexFiles:
outputFile:
refOnly:
searchType:
multithread:
ignore_multi_hits:
extract_matching_reads:

void FTSearch::overrideUtils(std::shared_ptr< IUtils > utils)¶

void FTSearch::overrideStats(std::shared_ptr< IStats > stats)¶

void FTSearch::overrideWriterBridge(std::shared_ptr< IWriterBridge > writerBridge)¶

void FTSearch::overrideKmerGenerator(std::shared_ptr< IKmerGenerator > kmerGenerator)¶

void FTSearch::overrideFinder(std::shared_ptr< IFinder > finder)¶

void FTSearch::overrideResultProcessor(std::shared_ptr< IResultProcessor > resultProcessor)¶

void FTSearch::overrideQueryExtractor(std::shared_ptr< IQueryExtractor > queryExtractor)¶

Private Members

fs::path FTSearch::_readFile¶: _readFile

std::map<std::string, uint> FTSearch::_counter¶: _counter

Utils FTSearch::_ownedUtils¶: _utils

IUtils* FTSearch::_utils¶

Stats FTSearch::_ownedStats¶: _stats

IStats* FTSearch::_stats¶

WriterBridge FTSearch::_ownedWriterBridge¶: _writerBridge

IWriterBridge* FTSearch::_writerBridge¶

KmerGenerator FTSearch::_ownedKmerGenerator¶: _kmerGenerator

IKmerGenerator* FTSearch::_kmerGenerator¶

Finder FTSearch::_ownedFinder¶: _finder

IFinder* FTSearch::_finder¶

ResultProcessor FTSearch::_ownedResultProcessor¶: _resultProcessor

IResultProcessor* FTSearch::_resultProcessor¶

QueryExtractor FTSearch::_ownedQueryExtractor¶: _queryExtractor

IQueryExtractor* FTSearch::_queryExtractor¶