BitMagic-C++: DNA_FingerprintScanner Class Reference

BitMagic-C++

Utility for keeping all DNA finger print vectors and search using various techniques. More...

Public Types
enum	{ eA = 0 , eC , eG , eT , eN , eEnd }

enum	{ eA = 0 , eC , eG , eT , eN , eEnd }

Public Member Functions
	DNA_FingerprintScanner ()

void	Build (const vector< char > &sequence)
	Build fingerprint bit-vectors from the original sequence. More...

const bm::bvector &	GetVector (char letter) const
	Return fingerprint bit-vector. More...

void	Find (const string &word, vector< unsigned > &res)
	Find word strings using shift + and on fingerprint vectors (horizontal, non-fused basic method) More...

void	FindAggFused (const string &word, vector< unsigned > &res)
	This method uses cache blocked aggregator with fused SHIFT+AND kernel. More...

void	FindCollection (const vector< tuple< string, int > > &words, vector< vector< unsigned >> &hits)
	Find a set of words in one pass using pipeline of aggregators (this is very experimental) More...

	DNA_FingerprintScanner ()

void	Build (const vector< char > &sequence)
	Build fingerprint bit-vectors from the original sequence. More...

void	BuildBulk (const vector< char > &sequence)
	Build index using bulk insert iterator. More...

void	BuildParallel (const vector< char > &sequence, unsigned threads)
	Build fingerprint bit-vectors using bulk insert iterator and parallel processing. More...

void	MergeVector (char letter, bm::bvector<> &bv)
	Thread sync bit-vector merge. More...

const bm::bvector &	GetVector (char letter) const
	Return fingerprint bit-vector. More...

Protected Member Functions
void	TranslateResults (const bm::bvector<> &bv, unsigned left_shift, vector< unsigned > &res)
	Translate search results vector using (word size) left shift. More...

Detailed Description

Utility for keeping all DNA finger print vectors and search using various techniques.

Examples: xsample04.cpp, xsample04a.cpp, and xsample07.cpp.

Definition at line 180 of file xsample04.cpp.

Member Enumeration Documentation

◆ anonymous enum

anonymous enum

Enumerator
eA
eC
eG
eT
eN
eEnd

Definition at line 183 of file xsample04.cpp.

◆ anonymous enum

anonymous enum

Enumerator
eA
eC
eG
eT
eN
eEnd

Definition at line 154 of file xsample04a.cpp.

Member Function Documentation

◆ Build() [1/2]

void DNA_FingerprintScanner::Build ( const vector< char > & sequence )

inline

Build fingerprint bit-vectors from the original sequence.

Examples: xsample04.cpp, and xsample04a.cpp.

Definition at line 189 of file xsample04.cpp.

References bm::BM_SORTED, eA, eC, eG, eN, and eT.

Referenced by main().

◆ Build() [2/2]

void DNA_FingerprintScanner::Build ( const vector< char > & sequence )

inline

Build fingerprint bit-vectors from the original sequence.

Definition at line 160 of file xsample04a.cpp.

References eA, eC, eG, eN, eT, and bm::bvector< Alloc >::inserter().

◆ BuildBulk()

void DNA_FingerprintScanner::BuildBulk ( const vector< char > & sequence )

inline

Build index using bulk insert iterator.

Examples: xsample04a.cpp.

Definition at line 196 of file xsample04a.cpp.

References bm::BM_SORTED, eA, eC, eG, eN, and eT.

Referenced by BuildParallel().

◆ BuildParallel()

void DNA_FingerprintScanner::BuildParallel	(	const vector< char > &	sequence,
		unsigned	threads
	)

inline

Build fingerprint bit-vectors using bulk insert iterator and parallel processing.

Examples: xsample04a.cpp, and xsample07.cpp.

Definition at line 234 of file xsample04a.cpp.

References bm::BM_SORTED, BuildBulk(), bm::bvector< Alloc >::bulk_insert_iterator::flush(), and MergeVector().

Referenced by main().

◆ Find()

void DNA_FingerprintScanner::Find	(	const string &	word,
		vector< unsigned > &	res
	)

inline

Find word strings using shift + and on fingerprint vectors (horizontal, non-fused basic method)

Examples: xsample04.cpp.

Definition at line 250 of file xsample04.cpp.

References bm::bvector< Alloc >::any(), GetVector(), bm::bvector< Alloc >::shift_right(), and TranslateResults().

Referenced by main().

◆ FindAggFused()

void DNA_FingerprintScanner::FindAggFused	(	const string &	word,
		vector< unsigned > &	res
	)

inline

This method uses cache blocked aggregator with fused SHIFT+AND kernel.

Examples: xsample04.cpp.

Definition at line 277 of file xsample04.cpp.

References bm::aggregator< BV >::add(), bm::aggregator< BV >::combine_shift_right_and(), GetVector(), bm::aggregator< BV >::reset(), and TranslateResults().

Referenced by main().

◆ FindCollection()

void DNA_FingerprintScanner::FindCollection	(	const vector< tuple< string, int > > &	words,
		vector< vector< unsigned >> &	hits
	)

inline

Find a set of words in one pass using pipeline of aggregators (this is very experimental)

Examples: xsample04.cpp.

Definition at line 302 of file xsample04.cpp.

References bm::aggregator_pipeline_execute(), bm::aggregator< bm::bvector<> >::BM_SHIFT_R_AND, bm::aggregator< BV >::get_target(), GetVector(), and TranslateResults().

Referenced by main().

◆ GetVector() [1/2]

const bm::bvector& DNA_FingerprintScanner::GetVector ( char letter ) const

inline

Return fingerprint bit-vector.

Examples: xsample04.cpp, and xsample04a.cpp.

Definition at line 226 of file xsample04.cpp.

References eA, eC, eG, eN, and eT.

Referenced by Find(), FindAggFused(), FindCollection(), and fingerprint_compare().

◆ GetVector() [2/2]

const bm::bvector& DNA_FingerprintScanner::GetVector ( char letter ) const

inline

Return fingerprint bit-vector.

Definition at line 371 of file xsample04a.cpp.

References eA, eC, eG, eN, and eT.

◆ MergeVector()

void DNA_FingerprintScanner::MergeVector	(	char	letter,
		bm::bvector<> &	bv
	)

inline

Thread sync bit-vector merge.

Examples: xsample04a.cpp.

Definition at line 324 of file xsample04a.cpp.

References eA, eC, eG, eN, eT, and bm::bvector< Alloc >::merge().

Referenced by BuildParallel().

◆ TranslateResults()

void DNA_FingerprintScanner::TranslateResults	(	const bm::bvector<> &	bv,
		unsigned	left_shift,
		vector< unsigned > &	res
	)

inlineprotected

Translate search results vector using (word size) left shift.

Examples: xsample04.cpp.

Definition at line 344 of file xsample04.cpp.

References bm::bvector< Alloc >::first(), and bm::bvector< Alloc >::iterator_base::valid().

Referenced by Find(), FindAggFused(), and FindCollection().

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