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

Inheritance diagram for DNA_FingerprintScanner:

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.
const bm::bvector &	GetVector (char letter) const
	Return fingerprint bit-vector.
void	Find (const string &word, vector< unsigned > &res)
	Find word strings using shift + and on fingerprint vectors (horizontal, non-fused basic method).
void	FindAggFused (const string &word, vector< unsigned > &res)
	This method uses cache blocked aggregator with fused SHIFT+AND kernel.
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).
	DNA_FingerprintScanner ()
void	Build (const vector< char > &sequence)
	Build fingerprint bit-vectors from the original sequence.
void	BuildBulk (const vector< char > &sequence)
	Build index using bulk insert iterator.
void	BuildParallel (const vector< char > &sequence, unsigned threads)
	Build fingerprint bit-vectors using bulk insert iterator and parallel processing.
void	MergeVector (char letter, bm::bvector<> &bv)
	Thread sync bit-vector merge.
const bm::bvector &	GetVector (char letter) const
	Return fingerprint bit-vector.

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

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 154 of file xsample04a.cpp.

◆ anonymous enum

anonymous enum

Enumerator
eA
eC
eG
eT
eN
eEnd

Definition at line 183 of file xsample04.cpp.

Constructor & Destructor Documentation

◆ DNA_FingerprintScanner() [1/2]

DNA_FingerprintScanner::DNA_FingerprintScanner ( )

inline

Examples: xsample04.cpp, and xsample04a.cpp.

Definition at line 185 of file xsample04.cpp.

◆ DNA_FingerprintScanner() [2/2]

DNA_FingerprintScanner::DNA_FingerprintScanner ( )

inline

Definition at line 156 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.

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.

◆ 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.

Referenced by DNA_FingerprintScanner< bm::bvector<> >::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.

Definition at line 234 of file xsample04a.cpp.

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.

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.

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.

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.

Referenced by DNA_FingerprintScanner< bm::bvector<> >::Find(), DNA_FingerprintScanner< bm::bvector<> >::FindAggFused(), DNA_FingerprintScanner< bm::bvector<> >::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.

◆ 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.

Referenced by DNA_FingerprintScanner< bm::bvector<> >::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.

Referenced by DNA_FingerprintScanner< bm::bvector<> >::Find(), DNA_FingerprintScanner< bm::bvector<> >::FindAggFused(), and DNA_FingerprintScanner< bm::bvector<> >::FindCollection().

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

Public Types

Public Member Functions

Protected Member Functions

Detailed Description

Member Enumeration Documentation

◆ anonymous enum

◆ anonymous enum

Constructor & Destructor Documentation

◆ DNA_FingerprintScanner() [1/2]

◆ DNA_FingerprintScanner() [2/2]

Member Function Documentation

◆ Build() [1/2]

◆ Build() [2/2]

◆ BuildBulk()

◆ BuildParallel()

◆ Find()

◆ FindAggFused()

◆ FindCollection()

◆ GetVector() [1/2]

◆ GetVector() [2/2]

◆ MergeVector()

◆ TranslateResults()