Search Toolkit Book for CBlastKmerBuildIndex

#include <algo/blast/proteinkmer/blastkmerindex.hpp>

Inheritance diagram for CBlastKmerBuildIndex:

Collaboration diagram for CBlastKmerBuildIndex:

Public Member Functions
	CBlastKmerBuildIndex (CRef< CSeqDB > seqdb, int kmerSize=5, int numHashFct=32, int samples=0, int compress=2, int alphabet=0, int version=0, int chunkSize=150)
	Constructor. More...

	~CBlastKmerBuildIndex ()
	Destructor. More...

void	Build (int numThreads=1)
	Build the index. More...

Public Member Functions inherited from CObject
	CObject (void)
	Constructor. More...

	CObject (const CObject &src)
	Copy constructor. More...

virtual	~CObject (void)
	Destructor. More...

CObject &	operator= (const CObject &src) THROWS_NONE
	Assignment operator. More...

bool	CanBeDeleted (void) const THROWS_NONE
	Check if object can be deleted. More...

bool	IsAllocatedInPool (void) const THROWS_NONE
	Check if object is allocated in memory pool (not system heap) More...

bool	Referenced (void) const THROWS_NONE
	Check if object is referenced. More...

bool	ReferencedOnlyOnce (void) const THROWS_NONE
	Check if object is referenced only once. More...

void	AddReference (void) const
	Add reference to object. More...

void	RemoveReference (void) const
	Remove reference to object. More...

void	ReleaseReference (void) const
	Remove reference without deleting object. More...

virtual void	DoNotDeleteThisObject (void)
	Mark this object as not allocated in heap – do not delete this object. More...

virtual void	DoDeleteThisObject (void)
	Mark this object as allocated in heap – object can be deleted. More...

void *	operator new (size_t size)
	Define new operator for memory allocation. More...

void *	operator new[] (size_t size)
	Define new[] operator for 'array' memory allocation. More...

void	operator delete (void *ptr)
	Define delete operator for memory deallocation. More...

void	operator delete[] (void *ptr)
	Define delete[] operator for memory deallocation. More...

void *	operator new (size_t size, void *place)
	Define new operator. More...

void	operator delete (void ptr, void place)
	Define delete operator. More...

void *	operator new (size_t size, CObjectMemoryPool *place)
	Define new operator using memory pool. More...

void	operator delete (void ptr, CObjectMemoryPool place)
	Define delete operator. More...

virtual void	DebugDump (CDebugDumpContext ddc, unsigned int depth) const
	Define method for dumping debug information. More...

Public Member Functions inherited from CDebugDumpable
	CDebugDumpable (void)

virtual	~CDebugDumpable (void)

void	DebugDumpText (ostream &out, const string &bundle, unsigned int depth) const

void	DebugDumpFormat (CDebugDumpFormatter &ddf, const string &bundle, unsigned int depth) const

void	DumpToConsole (void) const

Private Member Functions
void	x_WriteDataFile (vector< vector< vector< uint32_t > > > &seq_hash, int num_seqs, CNcbiOfstream &data_file)
	Writes out the data file. More...

void	x_BuildIndex (string &name, int start=0, int number=0)
	BUild index for an individual BLAST volume. More...

Private Attributes
int	m_NumHashFct

int	m_NumBands
	Number of hash functions. More...

int	m_RowsPerBand
	Number of LSH bands. More...

int	m_KmerSize
	Number of rows per band. More...

CRef< CSeqDB >	m_SeqDB
	Residues in kmer. More...

bool	m_DoSeg
	BLAST database. More...

int	m_Samples
	Should Seg be run on sequences. More...

int	m_Compress
	Number of samples (Buhler only) More...

int	m_Alphabet
	Compress the arrays for Jaccard matches. More...

int	m_Version
	0 for 15 letters, 1 for 10 letters. More...

int	m_ChunkSize
	version of index file More...

Additional Inherited Members
Public Types inherited from CObject
enum	EAllocFillMode { eAllocFillNone = 1 , eAllocFillZero , eAllocFillPattern }
	Control filling of newly allocated memory. More...

typedef CObjectCounterLocker	TLockerType
	Default locker type for CRef. More...

typedef atomic< Uint8 >	TCounter
	Counter type is CAtomiCounter. More...

typedef Uint8	TCount
	Alias for value type of counter. More...

Static Public Member Functions inherited from CObject
static NCBI_XNCBI_EXPORT void	ThrowNullPointerException (void)
	Define method to throw null pointer exception. More...

static NCBI_XNCBI_EXPORT void	ThrowNullPointerException (const type_info &type)

static EAllocFillMode	GetAllocFillMode (void)

static void	SetAllocFillMode (EAllocFillMode mode)

static void	SetAllocFillMode (const string &value)
	Set mode from configuration parameter value. More...

Static Public Member Functions inherited from CDebugDumpable
static void	EnableDebugDump (bool on)

Static Public Attributes inherited from CObject
static const TCount	eCounterBitsCanBeDeleted = 1 << 0
	Define possible object states. More...

static const TCount	eCounterBitsInPlainHeap = 1 << 1
	Heap signature was found. More...

static const TCount	eCounterBitsPlaceMask
	Mask for 'in heap' state flags. More...

static const int	eCounterStep = 1 << 2
	Skip over the "in heap" bits. More...

static const TCount	eCounterValid = TCount(1) << (sizeof(TCount) * 8 - 2)
	Minimal value for valid objects (reference counter is zero) Must be a single bit value. More...

static const TCount	eCounterStateMask
	Valid object, and object in heap. More...

Protected Member Functions inherited from CObject
virtual void	DeleteThis (void)
	Virtual method "deleting" this object. More...

Detailed Description

Definition at line 51 of file blastkmerindex.hpp.

Constructor & Destructor Documentation

◆ CBlastKmerBuildIndex()

CBlastKmerBuildIndex::CBlastKmerBuildIndex	(	CRef< CSeqDB >	seqdb,
		int	kmerSize = `5`,
		int	numHashFct = `32`,
		int	samples = `0`,
		int	compress = `2`,
		int	alphabet = `0`,
		int	version = `0`,
		int	chunkSize = `150`
	)

Constructor.

Definition at line 108 of file blastkmerindex.cpp.

◆ ~CBlastKmerBuildIndex()

CBlastKmerBuildIndex::~CBlastKmerBuildIndex ( )

inline

Destructor.

Definition at line 66 of file blastkmerindex.hpp.

Member Function Documentation

◆ Build()

void CBlastKmerBuildIndex::Build ( int numThreads = 1 )

Build the index.

Definition at line 461 of file blastkmerindex.cpp.

References CSeqDB::eProtein, CSeqDB::FindVolumePaths(), CSeqDB::GetDBNameList(), CSeqDB::GetNumSeqs(), last(), m_SeqDB, NULL, compile_time_bits::range(), CSeqDB::SetNumberOfThreads(), CDirEntry::SplitPath(), and x_BuildIndex().

Referenced by BOOST_AUTO_TEST_CASE(), and CBlastKmerBuildIndexApplication::Run().

◆ x_BuildIndex()

void CBlastKmerBuildIndex::x_BuildIndex	(	string &	name,
		int	start = `0`,
		int	number = `0`
	)

private

BUild index for an individual BLAST volume.

Definition at line 532 of file blastkmerindex.cpp.

References _ASSERT, a, b, GetKValues(), CSeqDB::GetNumSeqs(), GetRandomNumbers(), i, KMER_LSH_ARRAY_SIZE, m_Alphabet, m_ChunkSize, m_Compress, m_DoSeg, m_KmerSize, m_NumBands, m_NumHashFct, m_RowsPerBand, m_Samples, m_SeqDB, m_Version, NCBI_THROW, out(), s_BlastKmerLoadBadMers(), s_Get_LSH_index_hashes(), s_Get_LSH_index_hashes2(), s_Get_LSH_index_hashes5(), s_MinhashSequences(), s_MinhashSequences2(), ncbi::grid::netcache::search::fields::size, and x_WriteDataFile().

Referenced by Build().

◆ x_WriteDataFile()

void CBlastKmerBuildIndex::x_WriteDataFile	(	vector< vector< vector< uint32_t > > > &	seq_hash,
		int	num_seqs,
		CNcbiOfstream &	data_file
	)

private

Writes out the data file.

Definition at line 762 of file blastkmerindex.cpp.

References b, m_Compress, m_NumHashFct, m_Version, n, pearson_hash_int2byte(), pearson_hash_int2short(), and ct::sort().

Referenced by x_BuildIndex().

Member Data Documentation

◆ m_Alphabet

int CBlastKmerBuildIndex::m_Alphabet

private

Compress the arrays for Jaccard matches.

Definition at line 93 of file blastkmerindex.hpp.

Referenced by x_BuildIndex().

◆ m_ChunkSize

int CBlastKmerBuildIndex::m_ChunkSize

private

version of index file

Definition at line 97 of file blastkmerindex.hpp.

Referenced by x_BuildIndex().

◆ m_Compress

int CBlastKmerBuildIndex::m_Compress

private

Number of samples (Buhler only)

Definition at line 91 of file blastkmerindex.hpp.

Referenced by x_BuildIndex(), and x_WriteDataFile().

◆ m_DoSeg

bool CBlastKmerBuildIndex::m_DoSeg

private

BLAST database.

Definition at line 87 of file blastkmerindex.hpp.

Referenced by x_BuildIndex().

◆ m_KmerSize

int CBlastKmerBuildIndex::m_KmerSize

private

Number of rows per band.

Definition at line 83 of file blastkmerindex.hpp.

Referenced by x_BuildIndex().

◆ m_NumBands

int CBlastKmerBuildIndex::m_NumBands

private

Number of hash functions.

Definition at line 79 of file blastkmerindex.hpp.

Referenced by x_BuildIndex().

◆ m_NumHashFct

int CBlastKmerBuildIndex::m_NumHashFct

private

Definition at line 77 of file blastkmerindex.hpp.

Referenced by x_BuildIndex(), and x_WriteDataFile().

◆ m_RowsPerBand

int CBlastKmerBuildIndex::m_RowsPerBand

private

Number of LSH bands.

Definition at line 81 of file blastkmerindex.hpp.

Referenced by x_BuildIndex().

◆ m_Samples

int CBlastKmerBuildIndex::m_Samples

private

Should Seg be run on sequences.

Definition at line 89 of file blastkmerindex.hpp.

Referenced by x_BuildIndex().

◆ m_SeqDB

CRef<CSeqDB> CBlastKmerBuildIndex::m_SeqDB

private

Residues in kmer.

Definition at line 85 of file blastkmerindex.hpp.

Referenced by Build(), and x_BuildIndex().

◆ m_Version

int CBlastKmerBuildIndex::m_Version

private

0 for 15 letters, 1 for 10 letters.

Definition at line 95 of file blastkmerindex.hpp.

Referenced by x_BuildIndex(), and x_WriteDataFile().

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

include/algo/blast/proteinkmer/blastkmerindex.hpp
src/algo/blast/proteinkmer/blastkmerindex.cpp

Public Member Functions

Private Member Functions

Private Attributes

Additional Inherited Members

Detailed Description

Constructor & Destructor Documentation

◆ CBlastKmerBuildIndex()

◆ ~CBlastKmerBuildIndex()

Member Function Documentation

◆ Build()

◆ x_BuildIndex()

◆ x_WriteDataFile()

Member Data Documentation

◆ m_Alphabet

◆ m_ChunkSize

◆ m_Compress

◆ m_DoSeg

◆ m_KmerSize

◆ m_NumBands

◆ m_NumHashFct

◆ m_RowsPerBand

◆ m_Samples

◆ m_SeqDB

◆ m_Version