Search Toolkit Book for CLocalVDBBlast

#include <algo/blast/vdb/vdbblast_local.hpp>

Inheritance diagram for CLocalVDBBlast:

Collaboration diagram for CLocalVDBBlast:

Classes
struct	SLocalVDBStruct

Public Types
enum	ESRASearchMode { eUnaligned = 0 , eAligned = 1 , eBoth = 2 }

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...

Public Member Functions
	CLocalVDBBlast (CRef< CBlastQueryVector > query_vector, CRef< CBlastOptionsHandle > options, CLocalVDBBlast::SLocalVDBStruct &local_vdb, bool include_filtered_reads=false)

	CLocalVDBBlast (CRef< objects::CPssmWithParameters > pssm, CRef< CBlastOptionsHandle > options, SLocalVDBStruct &local_vdb, bool include_filtered_reads=false)

CRef< CSearchResultSet >	Run ()

Int4	GetNumExtensions ()

	~CLocalVDBBlast ()

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

Static Public Member Functions
static string	PreprocessDBs (CLocalVDBBlast::SLocalVDBStruct &local_vdb, const string db_names, unsigned int num_threads=kDisableThreadedSearch, ESRASearchMode seach_mode=eAligned)

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
static const unsigned int	kDisableThreadedSearch = 1

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...

Private Member Functions
	CLocalVDBBlast (const CLocalVDBBlast &)

CLocalVDBBlast &	operator= (const CLocalVDBBlast &)

CRef< CSearchResultSet >	RunThreadedSearch ()

void	x_AdjustDbSize (void)

void	x_PrepareQuery (vector< CRef< IQueryFactory > > &qf_v)

void	x_PreparePssm (vector< CRef< CPssmWithParameters > > &pssm)

Private Attributes
CRef< CBlastQueryVector >	m_query_vector

CRef< CBlastOptionsHandle >	m_opt_handle

Uint8	m_total_num_seqs

Uint8	m_total_length

vector< vector< string > > &	m_chunks_for_thread

unsigned int	m_num_threads

Int4	m_num_extensions

bool	m_include_filtered_reads

CRef< objects::CPssmWithParameters >	m_pssm

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

Detailed Description

Definition at line 43 of file vdbblast_local.hpp.

Member Enumeration Documentation

◆ ESRASearchMode

enum CLocalVDBBlast::ESRASearchMode

Enumerator
eUnaligned
eAligned
eBoth

Definition at line 102 of file vdbblast_local.hpp.

Constructor & Destructor Documentation

◆ CLocalVDBBlast() [1/3]

CLocalVDBBlast::CLocalVDBBlast ( const CLocalVDBBlast & )

private

◆ CLocalVDBBlast() [2/3]

CLocalVDBBlast::CLocalVDBBlast	(	CRef< CBlastQueryVector >	query_vector,
		CRef< CBlastOptionsHandle >	options,
		CLocalVDBBlast::SLocalVDBStruct &	local_vdb,
		bool	include_filtered_reads = `false`
	)

Definition at line 365 of file vdbblast_local.cpp.

◆ CLocalVDBBlast() [3/3]

CLocalVDBBlast::CLocalVDBBlast	(	CRef< objects::CPssmWithParameters >	pssm,
		CRef< CBlastOptionsHandle >	options,
		SLocalVDBStruct &	local_vdb,
		bool	include_filtered_reads = `false`
	)

Definition at line 381 of file vdbblast_local.cpp.

◆ ~CLocalVDBBlast()

CLocalVDBBlast::~CLocalVDBBlast ( )

inline

Definition at line 122 of file vdbblast_local.hpp.

Member Function Documentation

◆ GetNumExtensions()

Int4 CLocalVDBBlast::GetNumExtensions ( )

Definition at line 849 of file vdbblast_local.cpp.

References m_num_extensions.

Referenced by CVDBBlastnApp::Run().

◆ operator=()

CLocalVDBBlast& CLocalVDBBlast::operator= ( const CLocalVDBBlast & )

private

◆ PreprocessDBs()

string CLocalVDBBlast::PreprocessDBs	(	CLocalVDBBlast::SLocalVDBStruct &	local_vdb,
		const string	db_names,
		unsigned int	num_threads = `kDisableThreadedSearch`,
		ESRASearchMode	seach_mode = `eAligned`
	)

static

◆ Run()

CRef< CSearchResultSet > CLocalVDBBlast::Run ( void )

◆ RunThreadedSearch()

CRef< CSearchResultSet > CLocalVDBBlast::RunThreadedSearch ( void )

private

Definition at line 800 of file vdbblast_local.cpp.

References CBlastOptions::Clone(), eUnknown, CBlastOptions::GetHitlistSize(), CBlastOptionsHandle::GetOptions(), m_chunks_for_thread, m_include_filtered_reads, m_num_extensions, m_num_threads, m_opt_handle, m_pssm, NCBI_THROW, CRef< C, Locker >::NotEmpty(), NULL, results, s_CombineSearchSets(), CBlastOptionsHandle::SetOptions(), t, x_PreparePssm(), and x_PrepareQuery().

Referenced by Run().

◆ x_AdjustDbSize()

void CLocalVDBBlast::x_AdjustDbSize ( void )

private

Definition at line 654 of file vdbblast_local.cpp.

References CBlastOptions::GetDbLength(), CBlastOptions::GetEffectiveSearchSpace(), CBlastOptionsHandle::GetOptions(), kDisableThreadedSearch, m_chunks_for_thread, m_num_threads, m_opt_handle, m_total_length, m_total_num_seqs, CBlastOptions::SetDbLength(), CBlastOptions::SetDbSeqNum(), CBlastOptionsHandle::SetOptions(), and ncbi::grid::netcache::search::fields::size.

Referenced by Run().

◆ x_PreparePssm()

void CLocalVDBBlast::x_PreparePssm ( vector< CRef< CPssmWithParameters > > & pssm )

private

Definition at line 754 of file vdbblast_local.cpp.

References m_num_threads, m_pssm, MSerial_AsnBinary, and CRef< C, Locker >::Reset().

Referenced by RunThreadedSearch().

◆ x_PrepareQuery()

void CLocalVDBBlast::x_PrepareQuery ( vector< CRef< IQueryFactory > > & qf_v )

private

Definition at line 780 of file vdbblast_local.cpp.

References CBlastOptionsHandle::GetOptions(), ILocalQueryData::GetSequenceBlk(), m_num_threads, m_opt_handle, m_query_vector, IQueryFactory::MakeLocalQueryData(), and s_CloneBlastQueryVector().

Referenced by RunThreadedSearch().

Member Data Documentation

◆ kDisableThreadedSearch

const unsigned int CLocalVDBBlast::kDisableThreadedSearch = 1

static

Definition at line 67 of file vdbblast_local.hpp.

Referenced by PreprocessDBs(), Run(), and x_AdjustDbSize().

◆ m_chunks_for_thread

vector<vector<string> >& CLocalVDBBlast::m_chunks_for_thread

private

Definition at line 59 of file vdbblast_local.hpp.

Referenced by Run(), RunThreadedSearch(), and x_AdjustDbSize().

◆ m_include_filtered_reads

bool CLocalVDBBlast::m_include_filtered_reads

private

Definition at line 62 of file vdbblast_local.hpp.

Referenced by Run(), and RunThreadedSearch().

◆ m_num_extensions

Int4 CLocalVDBBlast::m_num_extensions

private

Definition at line 61 of file vdbblast_local.hpp.

Referenced by GetNumExtensions(), Run(), and RunThreadedSearch().

◆ m_num_threads

unsigned int CLocalVDBBlast::m_num_threads

private

Definition at line 60 of file vdbblast_local.hpp.

Referenced by Run(), RunThreadedSearch(), x_AdjustDbSize(), x_PreparePssm(), and x_PrepareQuery().

◆ m_opt_handle

CRef<CBlastOptionsHandle> CLocalVDBBlast::m_opt_handle

private

Definition at line 56 of file vdbblast_local.hpp.

Referenced by Run(), RunThreadedSearch(), x_AdjustDbSize(), and x_PrepareQuery().

◆ m_pssm

CRef<objects::CPssmWithParameters> CLocalVDBBlast::m_pssm

private

Definition at line 63 of file vdbblast_local.hpp.

Referenced by Run(), RunThreadedSearch(), and x_PreparePssm().

◆ m_query_vector

CRef<CBlastQueryVector> CLocalVDBBlast::m_query_vector

private

Definition at line 55 of file vdbblast_local.hpp.

Referenced by Run(), and x_PrepareQuery().

◆ m_total_length

Uint8 CLocalVDBBlast::m_total_length

private

Definition at line 58 of file vdbblast_local.hpp.

Referenced by x_AdjustDbSize().

◆ m_total_num_seqs

Uint8 CLocalVDBBlast::m_total_num_seqs

private

Definition at line 57 of file vdbblast_local.hpp.

Referenced by x_AdjustDbSize().

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

include/algo/blast/vdb/vdbblast_local.hpp
src/algo/blast/vdb/vdbblast_local.cpp

Classes

Public Types

Public Member Functions

Static Public Member Functions

Static Public Attributes

Private Member Functions

Private Attributes

Additional Inherited Members

Detailed Description

Member Enumeration Documentation

◆ ESRASearchMode

Constructor & Destructor Documentation

◆ CLocalVDBBlast() [1/3]

◆ CLocalVDBBlast() [2/3]

◆ CLocalVDBBlast() [3/3]

◆ ~CLocalVDBBlast()

Member Function Documentation

◆ GetNumExtensions()

◆ operator=()

◆ PreprocessDBs()

◆ Run()

◆ RunThreadedSearch()

◆ x_AdjustDbSize()

◆ x_PreparePssm()

◆ x_PrepareQuery()

Member Data Documentation

◆ kDisableThreadedSearch

◆ m_chunks_for_thread

◆ m_include_filtered_reads

◆ m_num_extensions

◆ m_num_threads

◆ m_opt_handle

◆ m_pssm

◆ m_query_vector

◆ m_total_length

◆ m_total_num_seqs