IKmerGenerator

IKmerGenerator.h

namespace ft

Copyright (c) 2018, Wasserman lab

FILE ikmergenerator.h

DESCRIPTION This file contains the declaration of kmergenerator interface

class IKmerGenerator

#include <ikmergenerator.h>

This file contains the declaration of kmergenerator interface.

Copyright

Copyright (c) 2019, Wasserman lab

Author

Godfrain Jacques Kounkou

Subclassed by ft::KmerGenerator

Public Functions

virtual std::set<std::string> ft::IKmerGenerator::genSlidingSearchStrings(const std::string & queryString, uint kmerSize, uint stride, bool kmerCounts, uint maxKmers)= 0

genSlidingSearchStrings

Return

Parameters

• queryString:
• kmerSize:
• stride:

virtual std::set<std::string> ft::IKmerGenerator::genCenteredSearchStrings(const std::string & queryString, uint kmerSize, uint overlap, uint stride, bool kmerCounts, uint maxKmers)= 0

genCenteredSearchStrings

Return

Parameters

• queryString:
• kmerSize:
• overlap:
• stride:

virtual SearchKmers ft::IKmerGenerator::genQueryKmers(Query inputQuery, uint kmerSize, bool refOnly, SearchType searchType, uint overlap, uint stride, bool crossover, bool kmerCounts, uint maxKmers)= 0

KmerGenerator::genQueryKmers.

Return

Parameters

• inputQuery:
• kmerSize:
• refOnly:
• searchType:
• overlap:
• stride:
• crossover:

virtual SearchKmers ft::IKmerGenerator::genSearchKmers(std::set< Query > inputQueries, uint kmerSize, bool refOnly, SearchType searchType, uint overlap, uint stride, bool kmerCounts, uint maxKmers)= 0

genSearchKmers

Return

Parameters

• inputQueries:
• kmerSize:
• refOnly:
• searchType:
• overlap:
• stride:

virtual void ft::IKmerGenerator::addtoKmerMap(KmerMap & kmerMap, const SearchKmers & queryKmers)= 0

KmerGenerator::addtoKmerMap.

Parameters

• kmerMap:
• queryKmers:

virtual void ft::IKmerGenerator::genKmerMap(std::set< Query > & inputQueries, uint kmerSize, bool refOnly, const SearchType & searchType, KmerMap & kmerMap, uint overlap, uint stride, bool crossover, bool ignoreNonUniqueKmers, bool kmerCounts, uint maxKmers, uint maxTotalKmers)= 0

KmerGenerator::genKmerMap.

Parameters

• inputQueries:
• kmerSize:
• refOnly:
• searchType:
• kmerMap:
• overlap:
• stride:
• crossover:
• ignoreNonUniqueKmers: