Search Toolkit Book for CCachedSequence

Manages a TSE and its subordinate chunks for all implementations of the IBlastDbAdapter interface. More...

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

Inheritance diagram for CCachedSequence:

Collaboration diagram for CCachedSequence:

Public Types
typedef vector< CRef< CTSE_Chunk_Info > >	TCTSE_Chunk_InfoVector
	A list of 'chunk' objects, generic sequence related data elements. 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...

Public Member Functions
	CCachedSequence (IBlastDbAdapter &blastdb, const CSeq_id_Handle &idh, int oid, bool use_fixed_size_slices, TSeqPos slice_size=kSequenceSliceSize)
	Construct and pre-process the sequence. More...

void	RegisterIds (CBlastDbDataLoader::TIdMap &idmap)
	Add this sequence's identifiers to a lookup table held by the data loader. More...

void	SplitSeqData (TCTSE_Chunk_InfoVector &chunks)
	Load or split the sequence data chunks. More...

CRef< CSeq_entry >	GetTSE () const
	Get the top-level seq-entry managed by this object. 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_AddSplitSeqChunk (TCTSE_Chunk_InfoVector &chunks, const CSeq_id_Handle &id, TSeqPos begin, TSeqPos end)
	Add a chunk of sequence data. More...

void	x_AddFullSeq_data (void)
	Add an the entire sequence data to this object's TSE as raw data in its Seq-data field. More...

Private Attributes
CSeq_id_Handle	m_SIH
	SeqID handle. More...

CRef< CSeq_entry >	m_TSE
	The Seq entry we handle. More...

TSeqPos	m_Length
	Sequence length in bases. More...

IBlastDbAdapter &	m_BlastDb
	Database reference. More...

int	m_OID
	Locates this sequence within m_BlastDb. More...

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

TSeqPos	m_SliceSize
	Specifies the slice size for splitting the sequence data. More...

Additional Inherited Members
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

Manages a TSE and its subordinate chunks for all implementations of the IBlastDbAdapter interface.

Definition at line 46 of file cached_sequence.hpp.

Member Typedef Documentation

◆ TCTSE_Chunk_InfoVector

typedef vector< CRef<CTSE_Chunk_Info> > CCachedSequence::TCTSE_Chunk_InfoVector

A list of 'chunk' objects, generic sequence related data elements.

Definition at line 81 of file cached_sequence.hpp.

Constructor & Destructor Documentation

◆ CCachedSequence()

CCachedSequence::CCachedSequence	(	IBlastDbAdapter &	blastdb,
		const CSeq_id_Handle &	idh,
		int	oid,
		bool	use_fixed_size_slices,
		TSeqPos	slice_size = `kSequenceSliceSize`
	)

Construct and pre-process the sequence.

This constructor starts the processing of the specified sequence. It loads the bioseq (minus sequence data) and caches the sequence length.

Parameters

idh	A handle to the sequence identifier.
blastdb	The interface to the BLAST database containing the original sequence.
oid	Locates the sequence within the BLAST database.
use_fixed_size_slices	Determines the strategy to retrieve the sequence data that is split, see comment for this class' m_UseFixedSizeSlices field.
slice_size	Determines the slice size for splitting the sequence data.

Definition at line 46 of file cached_sequence.cpp.

References _ASSERT, CSeq_inst_Base::eMol_aa, CSeq_inst_Base::eMol_na, CSeqDB::eProtein, CBioseq::GetFirstId(), CSeq_id_Handle::GetHandle(), CBioseq_Base::SetInst(), and ZERO_GI.

Member Function Documentation

◆ GetTSE()

CRef<CSeq_entry> CCachedSequence::GetTSE ( void ) const

inline

Get the top-level seq-entry managed by this object.

Definition at line 95 of file cached_sequence.hpp.

References m_TSE.

◆ RegisterIds()

void CCachedSequence::RegisterIds ( CBlastDbDataLoader::TIdMap & idmap )

Add this sequence's identifiers to a lookup table held by the data loader.

This method adds identifiers from this sequence to a lookup table so that the OID of the sequence can be found quickly during future processing of the same sequence.

Parameters

idmap A map from CSeq_id_Handle to OID.

Definition at line 98 of file cached_sequence.cpp.

References _ASSERT, CSeq_id_Handle::GetHandle(), CSeq_entry_Base::IsSeq(), ITERATE, m_OID, m_TSE, s_ExtractSeqIds(), CBioseq_Base::SetId(), and CSeq_entry_Base::SetSeq().

◆ SplitSeqData()

void CCachedSequence::SplitSeqData ( TCTSE_Chunk_InfoVector & chunks )

Load or split the sequence data chunks.

The sequence data is stored and a list of the available ranges of data is returned via the 'chunks' parameter. For large sequences, these do not contain sequence data, but merely indicate what is available, in other cases, the entire sequence data will be loaded

Parameters

chunks The sequence data chunks will be returned here.

Definition at line 120 of file cached_sequence.cpp.

References delta(), CSeq_inst_Base::eRepr_delta, CSeq_inst_Base::eRepr_raw, kFastSequenceLoadSize, kRmtSequenceSliceSize, kSliceGrowthFactor, m_Length, m_SIH, m_SliceSize, m_TSE, m_UseFixedSizeSlices, CSeq_inst_Base::SetExt(), CBioseq_Base::SetInst(), CSeq_inst_Base::SetRepr(), CSeq_entry_Base::SetSeq(), x_AddFullSeq_data(), and x_AddSplitSeqChunk().

◆ x_AddFullSeq_data()

void CCachedSequence::x_AddFullSeq_data ( void )

private

Add an the entire sequence data to this object's TSE as raw data in its Seq-data field.

Definition at line 112 of file cached_sequence.cpp.

References _ASSERT, IBlastDbAdapter::GetSequence(), m_BlastDb, m_Length, m_OID, m_TSE, CRef< C, Locker >::NotEmpty(), CBioseq_Base::SetInst(), and CSeq_entry_Base::SetSeq().

Referenced by SplitSeqData().

◆ x_AddSplitSeqChunk()

void CCachedSequence::x_AddSplitSeqChunk	(	TCTSE_Chunk_InfoVector &	chunks,
		const CSeq_id_Handle &	id,
		TSeqPos	begin,
		TSeqPos	end
	)

private

Add a chunk of sequence data.

This method builds a description of a specific range of sequence data, returning it via the 'chunks' parameter. The actual data is not built, just a description that identifies the sequence and the range of that sequence's data represented by this chunk.

Parameters

chunks	object where to add the chunk [in\|out]
id	identifier for the sequence chunk about to be added [in]
begin	starting offset of the chunk [in]
end	ending offset of the chunk [in]

Definition at line 157 of file cached_sequence.cpp.

References CTSE_Chunk_Info::x_AddSeq_data().

Referenced by SplitSeqData().

Member Data Documentation

◆ m_BlastDb

IBlastDbAdapter& CCachedSequence::m_BlastDb

private

Database reference.

Definition at line 110 of file cached_sequence.hpp.

Referenced by x_AddFullSeq_data().

◆ m_Length

TSeqPos CCachedSequence::m_Length

private

Sequence length in bases.

Definition at line 107 of file cached_sequence.hpp.

Referenced by SplitSeqData(), and x_AddFullSeq_data().

◆ m_OID

int CCachedSequence::m_OID

private

Locates this sequence within m_BlastDb.

Definition at line 113 of file cached_sequence.hpp.

Referenced by RegisterIds(), and x_AddFullSeq_data().

◆ m_SIH

CSeq_id_Handle CCachedSequence::m_SIH

private

SeqID handle.

Definition at line 101 of file cached_sequence.hpp.

Referenced by SplitSeqData().

◆ m_SliceSize

TSeqPos CCachedSequence::m_SliceSize

private

Specifies the slice size for splitting the sequence data.

Definition at line 122 of file cached_sequence.hpp.

Referenced by SplitSeqData().

◆ m_TSE

CRef<CSeq_entry> CCachedSequence::m_TSE

private

The Seq entry we handle.

Definition at line 104 of file cached_sequence.hpp.

Referenced by GetTSE(), RegisterIds(), SplitSeqData(), and x_AddFullSeq_data().

◆ m_UseFixedSizeSlices

bool CCachedSequence::m_UseFixedSizeSlices

private

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

The latter improves performance on full sequence retrieval of large sequences, but degrades the performance of retrieval of small sequence segments of large sequences

Definition at line 119 of file cached_sequence.hpp.

Referenced by SplitSeqData().

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

src/objtools/data_loaders/blastdb/cached_sequence.hpp
src/objtools/data_loaders/blastdb/cached_sequence.cpp

Public Types

Public Member Functions

Private Member Functions

Private Attributes

Additional Inherited Members

Detailed Description

Member Typedef Documentation

◆ TCTSE_Chunk_InfoVector

Constructor & Destructor Documentation

◆ CCachedSequence()

Member Function Documentation

◆ GetTSE()

◆ RegisterIds()

◆ SplitSeqData()

◆ x_AddFullSeq_data()

◆ x_AddSplitSeqChunk()

Member Data Documentation

◆ m_BlastDb

◆ m_Length

◆ m_OID

◆ m_SIH

◆ m_SliceSize

◆ m_TSE

◆ m_UseFixedSizeSlices