Search Toolkit Book for IBlastDbAdapter

Interface that provides a common interface to retrieve sequence data from local vs. More...

#include <objtools/data_loaders/blastdb/blastdb_adapter.hpp>

Inheritance diagram for IBlastDbAdapter:

Collaboration diagram for IBlastDbAdapter:

Public Types
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...

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

virtual CSeqDB::ESeqType	GetSequenceType ()=0
	Get the molecule type of this object (protein or nucleotide) More...

virtual int	GetSeqLength (int oid)=0
	Get the length of the sequence. More...

virtual list< CRef< CSeq_id > >	GetSeqIDs (int oid)=0
	Get the list of Seq-ids for the given OID. More...

virtual CRef< CBioseq >	GetBioseqNoData (int oid, TGi target_gi=ZERO_GI, const CSeq_id *target_id=NULL)=0
	Get a CBioseq for the requested oid, but without sequence data. More...

virtual CRef< CSeq_data >	GetSequence (int oid, int begin=0, int end=0)=0
	Get all or part of the sequence data as a Seq-data object. More...

virtual bool	SeqidToOid (const CSeq_id &id, int &oid)=0
	Find a Seq-id in the database and get an OID if found. 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

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

Interface that provides a common interface to retrieve sequence data from local vs.

remote BLAST databases.

Definition at line 68 of file blastdb_adapter.hpp.

Member Typedef Documentation

◆ TSeqIdList

typedef list< CRef<CSeq_id> > IBlastDbAdapter::TSeqIdList

Convenience typedef for a list of CSeq_id-s.

Definition at line 84 of file blastdb_adapter.hpp.

Constructor & Destructor Documentation

◆ ~IBlastDbAdapter()

virtual IBlastDbAdapter::~IBlastDbAdapter ( )

inlinevirtual

Virtual destructor.

Definition at line 72 of file blastdb_adapter.hpp.

Member Function Documentation

◆ GetBioseqNoData()

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

pure virtual

Get a CBioseq for the requested oid, but without sequence data.

If target is specified, that defline will be promoted to the top of the CBioseq object, if possible

Note: The current implementation of the remote BLAST database interface does not implement this promotion; the blast4 service will promote whichever Seq-id was used to fetch the OID, which in practice should be the same one.

Parameters

oid	An ID for this sequence in this db.
target_gi	If non-zero, the target GI to filter the header information.
target_id	if non-NULL, the target ID is used to filter the header information.

Returns: object corresponding to the sequence, but without sequence data.

Implemented in CRemoteBlastDbAdapter, and CLocalBlastDbAdapter.

◆ GetSeqIDs()

virtual list< CRef<CSeq_id> > IBlastDbAdapter::GetSeqIDs ( int oid )

pure virtual

Get the list of Seq-ids for the given OID.

Implemented in CRemoteBlastDbAdapter, and CLocalBlastDbAdapter.

Referenced by CBlastDbDataLoader::x_GetOid().

◆ GetSeqLength()

virtual int IBlastDbAdapter::GetSeqLength ( int oid )

pure virtual

Get the length of the sequence.

Parameters

oid	An ID for this sequence in this db.

Returns: Sequence length (in bases).

Implemented in CRemoteBlastDbAdapter, and CLocalBlastDbAdapter.

Referenced by CBlastDbDataLoader::GetSequenceLength().

◆ GetSequence()

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

pure virtual

Get all or part of the sequence data as a Seq-data object.

Parameters

oid	Identifies which sequence to get.
begin	Starting offset of the section to get.
end	Ending offset of the section to get.

Returns: The sequence data.

Note: if the begin and end arguments are zero, the whole sequence will be returned

Implemented in CRemoteBlastDbAdapter, and CLocalBlastDbAdapter.

Referenced by CreateSeqDataChunk(), and CCachedSequence::x_AddFullSeq_data().

◆ GetSequenceType()

virtual CSeqDB::ESeqType IBlastDbAdapter::GetSequenceType ( )

pure virtual

Get the molecule type of this object (protein or nucleotide)

Returns: The sequence type.

Implemented in CRemoteBlastDbAdapter, and CLocalBlastDbAdapter.

◆ GetTaxId()

virtual TTaxId IBlastDbAdapter::GetTaxId ( const CSeq_id_Handle & )

inlinevirtual

Retrieve the taxonomy ID for the requested sequence identifier.

Parameters

idh	The Seq-id for which to get the taxonomy ID

Returns: taxonomy ID if found, otherwise kInvalidSeqPos

Reimplemented in CLocalBlastDbAdapter.

Definition at line 131 of file blastdb_adapter.hpp.

References INVALID_TAX_ID.

Referenced by CBlastDbDataLoader::GetTaxId().

◆ SeqidToOid()

virtual bool IBlastDbAdapter::SeqidToOid	(	const CSeq_id &	id,
		int &	oid
	)

pure virtual

Find a Seq-id in the database and get an OID if found.

If the Seq-id is found, this method returns true, and the oid argument will be populated accordingly. This oid should be used in the other methods provided by this interface.

Parameters

id	The Seq-id to find.
oid	An ID for this sequence (if it was found).

Returns: True if the sequence was found in the database.

Implemented in CRemoteBlastDbAdapter, and CLocalBlastDbAdapter.

Referenced by CBlastDbDataLoader::GetSequenceLength(), and CBlastDbDataLoader::x_GetOid().

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

include/objtools/data_loaders/blastdb/blastdb_adapter.hpp

Public Types

Public Member Functions

Additional Inherited Members

Detailed Description

Member Typedef Documentation

◆ TSeqIdList

Constructor & Destructor Documentation

◆ ~IBlastDbAdapter()

Member Function Documentation

◆ GetBioseqNoData()

◆ GetSeqIDs()

◆ GetSeqLength()

◆ GetSequence()

◆ GetSequenceType()

◆ GetTaxId()

◆ SeqidToOid()