A class that creates the Kmers for a set of input queries.
#include <kmergenerator.h>
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| KmerGenerator (const uint &_kmerSize, const bool &_refOnly, const SearchType &_searchType, const uint &_overlap=0, const uint &_stride=1, const uint &_maxKmers=1000000000, const bool &_verbose=false) |
| | Constructor.
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virtual | ~KmerGenerator () |
| | Destructor.
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| virtual std::set< std::string > | genSlidingSearchStrings (const std::string &queryString) |
| | Generate search strings (i.e. kmers) for a sliding search. More...
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| virtual std::set< std::string > | genCenteredSearchStrings (const std::string &queryString) |
| | Generate search strings (i.e. kmers) for a centered search. More...
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| virtual std::set< std::string > | genSearchKmers (const ft::QueryClass &queryObj) |
| | Generate search strings (i.e. kmers) More...
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Constant functions to get properties for Kmer Generation
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uint | getKmerSize () const |
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bool | getRefOnly () const |
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SearchType | getSearchType () const |
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uint | getOverlap () const |
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uint | getStride () const |
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uint | getMaxKmers () const |
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std::map< std::string, uint > | _counter |
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uint | _kmerSize |
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bool | _refOnly |
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SearchType | _searchType |
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uint | _overlap |
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uint | _stride |
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uint | _maxKmers |
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bool | _verbose |
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◆ genCenteredSearchStrings()
| std::set< std::string > ft::KmerGenerator::genCenteredSearchStrings |
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const std::string & |
queryString | ) |
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virtual |
- Parameters
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- Returns
- set of kmers
◆ genSearchKmers()
| std::set< std::string > ft::KmerGenerator::genSearchKmers |
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const ft::QueryClass & |
queryObj | ) |
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- Parameters
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- Returns
- set of kmers
◆ genSlidingSearchStrings()
| std::set< std::string > ft::KmerGenerator::genSlidingSearchStrings |
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const std::string & |
queryString | ) |
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virtual |
- Parameters
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- Returns
- set of kmers
The documentation for this class was generated from the following files:
