Search Toolkit Book for CRemoteBlastDbAdapter

This class allows retrieval of sequence data from BLAST databases at NCBI. More...

#include "remote_blastdb_adapter.hpp"
(Private to src/objtools/data_loaders/blastdb.)

Inheritance diagram for CRemoteBlastDbAdapter:

Collaboration diagram for CRemoteBlastDbAdapter:

Public Member Functions
	CRemoteBlastDbAdapter (const string &db_name, CSeqDB::ESeqType db_type, bool use_fixed_size_slices)
	Constructor. More...

virtual CSeqDB::ESeqType	GetSequenceType ()
	@inheritDoc More...

virtual int	GetSeqLength (int oid)
	@inheritDoc More...

virtual TSeqIdList	GetSeqIDs (int oid)
	@inheritDoc More...

virtual CRef< CBioseq >	GetBioseqNoData (int oid, TGi target_gi=ZERO_GI, const CSeq_id *target_id=NULL)
	@inheritDoc More...

virtual CRef< CSeq_data >	GetSequence (int oid, int begin=0, int end=0)
	@inheritDoc More...

void	GetSequenceBatch (const vector< int > &oids, const vector< TSeqRange > &ranges, vector< CRef< CSeq_data > > &sequence_data)
	Batch-version of GetSequence. More...

virtual bool	SeqidToOid (const CSeq_id &id, int &oid)
	@inheritDoc More...

bool	SeqidToOidBatch (const vector< CRef< CSeq_id > > &ids, vector< int > &oids)
	Batch-version of SeqidToOid. More...

Public Member Functions inherited from IBlastDbAdapter
virtual	~IBlastDbAdapter ()
	Virtual destructor. More...

virtual TTaxId	GetTaxId (const CSeq_id_Handle &)
	Retrieve the taxonomy ID for the requested sequence identifier. 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_FetchData (int oid, int begin, int end)
	This method actually retrieves the sequence data. More...

void	x_FetchDataByBatch (const vector< int > &oids, const vector< TSeqRange > &ranges)

Private Attributes
string	m_DbName
	BLAST database name. More...

CSeqDB::ESeqType	m_DbType
	Sequence type of the BLAST database. More...

map< int, CCachedSeqDataForRemote >	m_Cache
	Internal cache, maps OIDs to CCachedSeqDataForRemote. More...

int	m_NextLocalId
	Our local "OID generator". More...

bool	m_UseFixedSizeSlices
	Determines whether sequences should be fetched in fixed size slices or in incrementally larger sizes. More...

Additional Inherited Members
Public Types inherited from IBlastDbAdapter
typedef list< CRef< CSeq_id > >	TSeqIdList
	Convenience typedef for a list of CSeq_id-s. More...

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

This class allows retrieval of sequence data from BLAST databases at NCBI.

Definition at line 178 of file remote_blastdb_adapter.hpp.

Constructor & Destructor Documentation

◆ CRemoteBlastDbAdapter()

CRemoteBlastDbAdapter::CRemoteBlastDbAdapter	(	const string &	db_name,
		CSeqDB::ESeqType	db_type,
		bool	use_fixed_size_slices
	)

Constructor.

Definition at line 47 of file remote_blastdb_adapter.cpp.

References CSeqDB::eProtein, CBlastServices::IsValidBlastDb(), NMacroArgs::kIsProtein, NCBI_THROW, and out().

Member Function Documentation

◆ GetBioseqNoData()

CRef< CBioseq > CRemoteBlastDbAdapter::GetBioseqNoData	(	int	oid,
		TGi	target_gi = `ZERO_GI`,
		const CSeq_id *	target_id = `NULL`
	)

virtual

@inheritDoc

Implements IBlastDbAdapter.

Definition at line 78 of file remote_blastdb_adapter.cpp.

References _ASSERT, CSerialObject::Assign(), GetBioseq(), IsValid(), and m_Cache.

◆ GetSeqIDs()

IBlastDbAdapter::TSeqIdList CRemoteBlastDbAdapter::GetSeqIDs ( int oid )

virtual

@inheritDoc

Implements IBlastDbAdapter.

Definition at line 71 of file remote_blastdb_adapter.cpp.

References _ASSERT, IsValid(), and m_Cache.

◆ GetSeqLength()

int CRemoteBlastDbAdapter::GetSeqLength ( int oid )

virtual

@inheritDoc

Implements IBlastDbAdapter.

Definition at line 64 of file remote_blastdb_adapter.cpp.

References _ASSERT, IsValid(), and m_Cache.

◆ GetSequence()

CRef< CSeq_data > CRemoteBlastDbAdapter::GetSequence	(	int	oid,
		int	begin = `0`,
		int	end = `0`
	)

virtual

@inheritDoc

Implements IBlastDbAdapter.

Definition at line 194 of file remote_blastdb_adapter.cpp.

References _ASSERT, CCachedSeqDataForRemote::GetSeqDataChunk(), CCachedSeqDataForRemote::HasSequenceData(), CCachedSeqDataForRemote::IsValid(), m_Cache, and x_FetchData().

◆ GetSequenceBatch()

void CRemoteBlastDbAdapter::GetSequenceBatch	(	const vector< int > &	oids,
		const vector< TSeqRange > &	ranges,
		vector< CRef< CSeq_data > > &	sequence_data
	)

Batch-version of GetSequence.

Parameters

oids	OIDs of the sequences to fetch, must be of same size as ranges [in]
ranges	sequence ranges for the OIDs above, must be of same size as oids. If any of the ranges is TSeqRange::GetEmpty, the whole sequence will be fetched (assuming no splitting of the sequence occurred), otherwise the ranges are expected to be spanning a give sequence chunk