Search Toolkit Book for CBlastDbDataLoader

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

Inheritance diagram for CBlastDbDataLoader:

Collaboration diagram for CBlastDbDataLoader:

Classes
struct	SBlastDbParam

Public Types
enum	EDbType { eNucleotide = 0 , eProtein = 1 , eUnknown = 2 }
	Describes the type of blast database to use. More...

typedef SRegisterLoaderInfo< CBlastDbDataLoader >	TRegisterLoaderInfo

typedef limited_size_map< CSeq_id_Handle, int >	TIdMap
	A mapping from sequence identifier to blob ids. More...

Public Types inherited from CDataLoader
enum	EChoice { eBlob , eBioseq , eCore , eBioseqCore , eSequence , eFeatures , eGraph , eAlign , eAnnot , eExtFeatures , eExtGraph , eExtAlign , eExtAnnot , eOrphanAnnot , eAll }
	main blob is blob with sequence all other blobs are external and contain external annotations More...

typedef CTSE_Lock	TTSE_Lock

typedef set< TTSE_Lock >	TTSE_LockSet

typedef CRef< CTSE_Chunk_Info >	TChunk

typedef vector< TChunk >	TChunkSet

typedef set< string >	TProcessedNAs

typedef set< CSeq_id_Handle >	TSeq_idSet

typedef vector< CSeq_id_Handle >	TIds

typedef vector< bool >	TLoaded
	Bulk loading interface for a small pieces of information per id. More...

typedef vector< TIds >	TBulkIds

typedef vector< TGi >	TGis

typedef vector< string >	TLabels

typedef vector< TTaxId >	TTaxIds

typedef vector< TSeqPos >	TSequenceLengths

typedef vector< CSeq_inst::TMol >	TSequenceTypes

typedef vector< int >	TSequenceStates

typedef vector< int >	TSequenceHashes

typedef vector< bool >	THashKnown

typedef map< CSeq_id_Handle, TTSE_LockSet >	TTSE_LockSets

typedef vector< vector< CSeq_id_Handle > >	TSeqIdSets

typedef vector< CTSE_Lock >	TCDD_Locks

typedef CBlobIdKey	TBlobId

typedef int	TBlobVersion

typedef CRef< IEditSaver >	TEditSaver

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	~CBlastDbDataLoader ()

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

virtual TTSE_LockSet	GetRecords (const CSeq_id_Handle &idh, EChoice choice)
	Load TSE. More...

virtual void	GetChunk (TChunk chunk)
	Load a description or data chunk. More...

virtual TTaxId	GetTaxId (const CSeq_id_Handle &idh)
	Request for a taxonomy id of a sequence. More...

virtual void	GetTaxIds (const TIds &ids, TLoaded &loaded, TTaxIds &ret)

virtual TSeqPos	GetSequenceLength (const CSeq_id_Handle &idh)
	Request for a length of a sequence. More...

virtual void	GetSequenceLengths (const TIds &ids, TLoaded &loaded, TSequenceLengths &ret)

virtual CSeq_inst::TMol	GetSequenceType (const CSeq_id_Handle &idh)
	Request for a type of a sequence Returns CSeq_inst::eMol_not_set if sequence is not known. More...

virtual void	GetSequenceTypes (const TIds &ids, TLoaded &loaded, TSequenceTypes &ret)

virtual TBlobId	GetBlobId (const CSeq_id_Handle &idh)
	Gets the blob id for a given sequence. More...

virtual bool	CanGetBlobById () const
	Test method for GetBlobById feature. More...

virtual TTSE_Lock	GetBlobById (const TBlobId &blob_id)
	For a given TBlobId, get the TTSE_Lock. More...

Public Member Functions inherited from CDataLoader
virtual	~CDataLoader (void)

TTSE_LockSet	GetRecordsNoBlobState (const CSeq_id_Handle &idh, EChoice choice)
	The same as GetRecords() but always returns empty TSE lock set instead of throwing CBlobStateException. More...

virtual TTSE_LockSet	GetDetailedRecords (const CSeq_id_Handle &idh, const SRequestDetails &details)
	Request from a datasource using handles and ranges instead of seq-loc The TSEs loaded in this call will be added to the tse_set. More...

virtual TTSE_LockSet	GetExternalRecords (const CBioseq_Info &bioseq)
	Request from a datasource set of blobs with external annotations. More...

virtual TTSE_LockSet	GetOrphanAnnotRecords (const CSeq_id_Handle &idh, const SAnnotSelector *sel)
	old Get*AnnotRecords() methods More...

virtual TTSE_LockSet	GetExternalAnnotRecords (const CSeq_id_Handle &idh, const SAnnotSelector *sel)

virtual TTSE_LockSet	GetExternalAnnotRecords (const CBioseq_Info &bioseq, const SAnnotSelector *sel)

virtual TTSE_LockSet	GetOrphanAnnotRecordsNA (const CSeq_id_Handle &idh, const SAnnotSelector sel, TProcessedNAs processed_nas)
	new Get*AnnotRecords() methods More...

virtual TTSE_LockSet	GetOrphanAnnotRecordsNA (const TSeq_idSet &ids, const SAnnotSelector sel, TProcessedNAs processed_nas)

virtual TTSE_LockSet	GetExternalAnnotRecordsNA (const CSeq_id_Handle &idh, const SAnnotSelector sel, TProcessedNAs processed_nas)

virtual TTSE_LockSet	GetExternalAnnotRecordsNA (const CBioseq_Info &bioseq, const SAnnotSelector sel, TProcessedNAs processed_nas)

virtual void	GetIds (const CSeq_id_Handle &idh, TIds &ids)
	Request for a list of all Seq-ids of a sequence. More...

bool	SequenceExists (const CSeq_id_Handle &idh)
	helper function to check if sequence exists, uses GetIds() More...

virtual CSeq_id_Handle	GetAccVer (const CSeq_id_Handle &idh)
	Request for a accession.version Seq-id of a sequence. More...

virtual SAccVerFound	GetAccVerFound (const CSeq_id_Handle &idh)

virtual TGi	GetGi (const CSeq_id_Handle &idh)
	Request for a gi of a sequence. More...

virtual SGiFound	GetGiFound (const CSeq_id_Handle &idh)

virtual string	GetLabel (const CSeq_id_Handle &idh)
	Request for a label string of a sequence. More...

virtual STypeFound	GetSequenceTypeFound (const CSeq_id_Handle &idh)

virtual int	GetSequenceState (const CSeq_id_Handle &idh)
	Request for a state of a sequence. More...

virtual int	GetSequenceHash (const CSeq_id_Handle &idh)
	Request for a sequence hash. More...

virtual SHashFound	GetSequenceHashFound (const CSeq_id_Handle &idh)

virtual void	GetBulkIds (const TIds &ids, TLoaded &loaded, TBulkIds &ret)
	Bulk request for all Seq-ids of a set of sequences. More...

virtual void	GetAccVers (const TIds &ids, TLoaded &loaded, TIds &ret)
	Bulk request for accession.version Seq-ids of a set of sequences. More...

virtual void	GetGis (const TIds &ids, TLoaded &loaded, TGis &ret)
	Bulk request for gis of a set of sequences. More...

virtual void	GetLabels (const TIds &ids, TLoaded &loaded, TLabels &ret)
	Bulk request for label strings of a set of sequences. More...

virtual void	GetTaxIds (const TIds &ids, TLoaded &loaded, TTaxIds &ret)
	Bulk request for taxonomy ids of a set of sequences. More...

virtual void	GetSequenceLengths (const TIds &ids, TLoaded &loaded, TSequenceLengths &ret)
	Bulk request for lengths of a set of sequences. More...

virtual void	GetSequenceTypes (const TIds &ids, TLoaded &loaded, TSequenceTypes &ret)
	Bulk request for types of a set of sequences. More...

virtual void	GetSequenceStates (const TIds &ids, TLoaded &loaded, TSequenceStates &ret)
	Bulk request for states of a set of sequences. More...

virtual void	GetSequenceHashes (const TIds &ids, TLoaded &loaded, TSequenceHashes &ret, THashKnown &known)
	Bulk request for hashes of a set of sequences. More...

virtual void	GetCDDAnnots (const TSeqIdSets &id_sets, TLoaded &loaded, TCDD_Locks &ret)

virtual void	GetBlobs (TTSE_LockSets &tse_sets)

virtual TBlobId	GetBlobIdFromString (const string &str) const

virtual TBlobVersion	GetBlobVersion (const TBlobId &id)

virtual SRequestDetails	ChoiceToDetails (EChoice choice) const

virtual EChoice	DetailsToChoice (const SRequestDetails::TAnnotSet &annots) const

virtual EChoice	DetailsToChoice (const SRequestDetails &details) const

virtual void	GetChunks (const TChunkSet &chunks)

virtual void	DropTSE (CRef< CTSE_Info > tse_info)

void	SetTargetDataSource (CDataSource &data_source)
	Specify datasource to send loaded data to. More...

string	GetName (void) const

virtual TTSE_Lock	ResolveConflict (const CSeq_id_Handle &id, const TTSE_LockSet &tse_set)
	Resolve TSE conflict *select the best TSE from the set of dead TSEs. More...

virtual void	GC (void)

virtual TEditSaver	GetEditSaver () const

virtual CObjectManager::TPriority	GetDefaultPriority (void) const

virtual Uint4	EstimateLoadBytes (const CTSE_Chunk_Info &chunk) const

virtual double	EstimateLoadSeconds (const CTSE_Chunk_Info &chunk, Uint4 bytes) const

virtual unsigned	GetDefaultBlobCacheSizeLimit () const

virtual bool	GetTrackSplitSeq () const

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...

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 TRegisterLoaderInfo	RegisterInObjectManager (CObjectManager &om, const string &dbname="nr", const EDbType dbtype=eUnknown, bool use_fixed_size_slices=true, CObjectManager::EIsDefault is_default=CObjectManager::eNonDefault, CObjectManager::TPriority priority=CObjectManager::kPriority_NotSet)

static TRegisterLoaderInfo	RegisterInObjectManager (CObjectManager &om, CRef< CSeqDB > db_handle, bool use_fixed_size_slices=true, CObjectManager::EIsDefault is_default=CObjectManager::eNonDefault, CObjectManager::TPriority priority=CObjectManager::kPriority_NotSet)

static string	GetLoaderNameFromArgs (CConstRef< CSeqDB > db_handle)

static string	GetLoaderNameFromArgs (const SBlastDbParam &param)

static string	GetLoaderNameFromArgs (const string &dbname="nr", const EDbType dbtype=eUnknown)

static TRegisterLoaderInfo	RegisterInObjectManager (CObjectManager &om, const string &dbname, const EDbType dbtype, CObjectManager::EIsDefault is_default, CObjectManager::TPriority priority=CObjectManager::kPriority_NotSet)

static TRegisterLoaderInfo	RegisterInObjectManager (CObjectManager &om, CRef< CSeqDB > db_handle, CObjectManager::EIsDefault is_default=CObjectManager::eNonDefault, CObjectManager::TPriority priority=CObjectManager::kPriority_NotSet)

Static Public Member Functions inherited from CDataLoader
static bool	IsRequestedAnyNA (const SAnnotSelector *sel)

static bool	IsRequestedNA (const string &na, const SAnnotSelector *sel)

static bool	IsProcessedNA (const string &na, const TProcessedNAs *processed_nas)

static void	SetProcessedNA (const string &na, TProcessedNAs *processed_nas)

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)

Protected Types
typedef int	TBioseq_setId
	TPlace is a Seq-id or an integer id, this data loader uses the former. More...

typedef CSeq_id_Handle	TBioseqId

typedef pair< TBioseqId, TBioseq_setId >	TPlace

typedef CParamLoaderMaker< CBlastDbDataLoader, SBlastDbParam >	TMaker

Protected Member Functions
	CBlastDbDataLoader ()
	Default (no-op) constructor. More...

	CBlastDbDataLoader (const string &loader_name, const SBlastDbParam &param)
	Parametrized constructor. More...

	CBlastDbDataLoader (const CBlastDbDataLoader &)
	Prevent automatic copy constructor generation. More...

CBlastDbDataLoader &	operator= (const CBlastDbDataLoader &)
	Prevent automatic assignment operator generation. More...

int	x_GetOid (const CSeq_id_Handle &idh)
	Gets the OID from m_Ids cache or the BLAST databases. More...

int	x_GetOid (const TBlobId &blob_id) const
	Gets the OID from a TBlobId (see typedef in bdbloader.cpp) More...

void	x_LoadData (const CSeq_id_Handle &idh, int oid, CTSE_LoadLock &lock, int slice_size)
	Load sequence data from cache or from the database. More...

Protected Member Functions inherited from CDataLoader
	CDataLoader (void)

	CDataLoader (const string &loader_name)

void	SetName (const string &loader_name)

CDataSource *	GetDataSource (void) const

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

Protected Attributes
string	m_DBName
	Blast database name. More...

EDbType	m_DBType
	Is this database protein or nucleotide? More...

CRef< IBlastDbAdapter >	m_BlastDb
	The sequence database. More...

TIdMap	m_Ids
	ID to OID translation. More...

bool	m_UseFixedSizeSlices
	Configuration value specified to the CCachedSequence. More...

Friends
class	CParamLoaderMaker< CBlastDbDataLoader, SBlastDbParam >

Additional Inherited Members
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...

Static Protected Member Functions inherited from CDataLoader
static void	RegisterInObjectManager (CObjectManager &om, CLoaderMaker_Base &loader_maker, CObjectManager::EIsDefault is_default, CObjectManager::TPriority priority)
	Register the loader only if the name is not yet registered in the object manager. More...

Detailed Description

Definition at line 53 of file bdbloader.hpp.

Member Typedef Documentation

◆ TBioseq_setId

typedef int CBlastDbDataLoader::TBioseq_setId

protected

TPlace is a Seq-id or an integer id, this data loader uses the former.

Definition at line 176 of file bdbloader.hpp.

◆ TBioseqId

typedef CSeq_id_Handle CBlastDbDataLoader::TBioseqId

protected

Definition at line 177 of file bdbloader.hpp.

◆ TIdMap

typedef limited_size_map<CSeq_id_Handle, int> CBlastDbDataLoader::TIdMap

A mapping from sequence identifier to blob ids.

Definition at line 155 of file bdbloader.hpp.

◆ TMaker

typedef CParamLoaderMaker<CBlastDbDataLoader, SBlastDbParam> CBlastDbDataLoader::TMaker

protected

Definition at line 180 of file bdbloader.hpp.

◆ TPlace

typedef pair<TBioseqId, TBioseq_setId> CBlastDbDataLoader::TPlace

protected

Definition at line 178 of file bdbloader.hpp.

◆ TRegisterLoaderInfo

typedef SRegisterLoaderInfo<CBlastDbDataLoader> CBlastDbDataLoader::TRegisterLoaderInfo

Definition at line 78 of file bdbloader.hpp.

Member Enumeration Documentation

◆ EDbType

enum CBlastDbDataLoader::EDbType

Describes the type of blast database to use.

Enumerator
eNucleotide	nucleotide database
eProtein	protein database
eUnknown	protein is attempted first, then nucleotide

Definition at line 57 of file bdbloader.hpp.

Constructor & Destructor Documentation

◆ ~CBlastDbDataLoader()

CBlastDbDataLoader::~CBlastDbDataLoader ( void )

virtual

Definition at line 203 of file bdbloader.cpp.

◆ CBlastDbDataLoader() [1/3]

CBlastDbDataLoader::CBlastDbDataLoader ( )

inlineprotected

Default (no-op) constructor.

Definition at line 184 of file bdbloader.hpp.

◆ CBlastDbDataLoader() [2/3]

CBlastDbDataLoader::CBlastDbDataLoader	(	const string &	loader_name,
		const SBlastDbParam &	param
	)

protected

Parametrized constructor.

Parameters

loader_name	name of this data loader [in]
param	parameters to initialize this data loader [in]

Definition at line 180 of file bdbloader.cpp.

References _ASSERT, _TRACE, DbTypeToSeqType(), CRef< C, Locker >::Empty(), GetLoaderNameFromArgs(), m_BlastDb, CBlastDbDataLoader::SBlastDbParam::m_BlastDbHandle, m_DBName, m_DBType, NCBI_THROW, CRef< C, Locker >::NotEmpty(), and CRef< C, Locker >::Reset().

◆ CBlastDbDataLoader() [3/3]

CBlastDbDataLoader::CBlastDbDataLoader ( const CBlastDbDataLoader & )

protected

Prevent automatic copy constructor generation.

Member Function Documentation

◆ CanGetBlobById()

bool CBlastDbDataLoader::CanGetBlobById ( void ) const

virtual

Test method for GetBlobById feature.

The caller will use this method to determine whether this data loader allows blobs to be managed by ID.

Returns: Returns true to indicate that GetBlobById() is available.

Reimplemented from CDataLoader.

Definition at line 434 of file bdbloader.cpp.

◆ DebugDump()

void CBlastDbDataLoader::DebugDump	(	CDebugDumpContext	ddc,
		unsigned int	depth
	)		const

virtual

Define method for dumping debug information.

Reimplemented from CObject.

Reimplemented in CRemoteBlastDbDataLoader.

Definition at line 466 of file bdbloader.cpp.

References DebugDumpValue(), m_DBName, m_DBType, m_UseFixedSizeSlices, and CDebugDumpContext::SetFrame().

◆ GetBlobById()

CBlastDbDataLoader::TTSE_Lock CBlastDbDataLoader::GetBlobById ( const TBlobId & blob_id )

virtual

For a given TBlobId, get the TTSE_Lock.

If the provided TBlobId is known to this code, the corresponding TTSE_Lock data will be fetched and returned. Otherwise, an empty valued TTSE_Lock is returned.

Parameters

blob_id Indicates which data to get.

Returns: The returned data.

Reimplemented from CDataLoader.

Reimplemented in CRemoteBlastDbDataLoader.

Definition at line 453 of file bdbloader.cpp.

References first(), CDataLoader::GetDataSource(), CDataSource::GetTSE_LoadLock(), CBlobIdFor< Value, Converter >::GetValue(), CTSE_LoadLock::IsLoaded(), kSequenceSliceSize, and x_LoadData().

Referenced by GetRecords().

◆ GetBlobId()

CBlastDbDataLoader::TBlobId CBlastDbDataLoader::GetBlobId ( const CSeq_id_Handle & idh )

virtual

Gets the blob id for a given sequence.

Given a Seq_id_Handle, this method finds the corresponding top level Seq-entry (TSE) and returns a blob corresponding to it. The BlobId is initialized with a pointer to that CSeq_entry if the sequence is known to this data loader, which will be true if GetRecords() was called for this sequence.

Parameters

idh	Indicates the sequence for which to get a blob id.

Returns: A TBlobId corresponding to the provided Seq_id_Handle.

Reimplemented from CDataLoader.

Definition at line 441 of file bdbloader.cpp.

References x_GetOid().

Referenced by GetRecords().

◆ GetChunk()

void CBlastDbDataLoader::GetChunk ( TChunk chunk )

virtual

Load a description or data chunk.

Reimplemented from CDataLoader.

Definition at line 360 of file bdbloader.cpp.

References _ASSERT, CreateSeqDataChunk(), CTSE_Chunk_Info::GetBlobId(), CTSE_Chunk_Info::GetSeq_dataInfos(), CTSE_Chunk_Info::IsLoaded(), ITERATE, m_BlastDb, CTSE_Chunk_Info::SetLoaded(), x_GetOid(), and CTSE_Chunk_Info::x_LoadSequence().

◆ GetLoaderNameFromArgs() [1/3]

string CBlastDbDataLoader::GetLoaderNameFromArgs ( CConstRef< CSeqDB > db_handle )

static

Definition at line 164 of file bdbloader.cpp.

References _ASSERT, DbTypeToStr(), CThread::GetSelf(), NStr::IntToString(), kPrefix, kPrefixThread, CConstRef< C, Locker >::NotEmpty(), and SeqTypeToDbType().

Referenced by BOOST_AUTO_TEST_CASE(), CBlastDbDataLoader(), CLBLASTObjectLoader::GetLoaderName(), CDLTestThread::Main(), RegisterOMDataLoader(), s_MTDataLoaderTest2(), and s_RegisterOMDataLoader().

◆ GetLoaderNameFromArgs() [2/3]

string CBlastDbDataLoader::GetLoaderNameFromArgs ( const SBlastDbParam & param )

static

Definition at line 152 of file bdbloader.cpp.

References DbTypeToStr(), CThread::GetSelf(), NStr::IntToString(), kPrefix, kPrefixThread, CBlastDbDataLoader::SBlastDbParam::m_DbName, and CBlastDbDataLoader::SBlastDbParam::m_DbType.

◆ GetLoaderNameFromArgs() [3/3]

static string CBlastDbDataLoader::GetLoaderNameFromArgs	(	const string &	dbname = `"nr"`,
		const EDbType	dbtype = `eUnknown`
	)

inlinestatic

Definition at line 94 of file bdbloader.hpp.

References dbname().

◆ GetRecords()

CBlastDbDataLoader::TTSE_LockSet CBlastDbDataLoader::GetRecords	(	const CSeq_id_Handle &	idh,
		EChoice	choice
	)

virtual

Load TSE.

Reimplemented from CDataLoader.

Definition at line 230 of file bdbloader.cpp.

References CDataLoader::eAll, CDataLoader::eBioseq, CDataLoader::eBioseqCore, CDataLoader::eBlob, CDataLoader::eCore, CDataLoader::eSequence, GetBlobById(), GetBlobId(), and set< Key, Compare >::insert().

◆ GetSequenceLength()

TSeqPos CBlastDbDataLoader::GetSequenceLength ( const CSeq_id_Handle & idh )

virtual

Request for a length of a sequence.

Returns kInvalidSeqPos if sequence with requested id is not known. The result must not be kInvalidSeqPos for existing sequences

Reimplemented from CDataLoader.

Definition at line 312 of file bdbloader.cpp.

References CSeq_id_Handle::GetSeqId(), IBlastDbAdapter::GetSeqLength(), kInvalidSeqPos, m_BlastDb, and IBlastDbAdapter::SeqidToOid().

Referenced by GetSequenceLengths().

◆ GetSequenceLengths()

void CBlastDbDataLoader::GetSequenceLengths	(	const TIds &	ids,
		TLoaded &	loaded,
		TSequenceLengths &	ret
	)

virtual

Definition at line 321 of file bdbloader.cpp.

References _ASSERT, GetSequenceLength(), and i.

◆ GetSequenceType()

CSeq_inst::TMol CBlastDbDataLoader::GetSequenceType ( const CSeq_id_Handle & idh )

virtual

Request for a type of a sequence Returns CSeq_inst::eMol_not_set if sequence is not known.

See also: GetSequenceTypeFound()

Reimplemented from CDataLoader.

Definition at line 336 of file bdbloader.cpp.

References CSeq_inst_Base::eMol_aa, CSeq_inst_Base::eMol_na, CSeq_inst_Base::eMol_not_set, eNucleotide, eProtein, and m_DBType.

◆ GetSequenceTypes()

void CBlastDbDataLoader::GetSequenceTypes	(	const TIds &	ids,
		TLoaded &	loaded,
		TSequenceTypes &	ret
	)

virtual

Definition at line 345 of file bdbloader.cpp.

References _ASSERT, CSeq_inst_Base::eMol_aa, CSeq_inst_Base::eMol_na, CSeq_inst_Base::eMol_not_set, eNucleotide, eProtein, and m_DBType.

◆ GetTaxId()

TTaxId CBlastDbDataLoader::GetTaxId ( const CSeq_id_Handle & idh )

virtual

Request for a taxonomy id of a sequence.

Returns -1 if sequence with requested id is not known. Returns 0 if existing sequence doesn't have TaxID

Reimplemented from CDataLoader.

Definition at line 292 of file bdbloader.cpp.

References IBlastDbAdapter::GetTaxId(), and m_BlastDb.

Referenced by GetTaxIds().

◆ GetTaxIds()

void CBlastDbDataLoader::GetTaxIds	(	const TIds &	ids,
		TLoaded &	loaded,
		TTaxIds &	ret
	)

virtual

Definition at line 297 of file bdbloader.cpp.

References _ASSERT, GetTaxId(), and i.

◆ operator=()

CBlastDbDataLoader& CBlastDbDataLoader::operator= ( const CBlastDbDataLoader & )

protected

Prevent automatic assignment operator generation.

◆ RegisterInObjectManager() [1/4]

CBlastDbDataLoader::TRegisterLoaderInfo CBlastDbDataLoader::RegisterInObjectManager	(	CObjectManager &	om,
		const string &	dbname,
		const EDbType	dbtype,
		CObjectManager::EIsDefault	is_default,
		CObjectManager::TPriority	priority = `CObjectManager::kPriority_NotSet`
	)

static

Note: this is added to temporarily comply with the toolkit's stable components rule of having backwards compatible APIs

Definition at line 81 of file bdbloader.cpp.

References dbname(), om, and RegisterInObjectManager().

◆ RegisterInObjectManager() [2/4]

CBlastDbDataLoader::TRegisterLoaderInfo CBlastDbDataLoader::RegisterInObjectManager	(	CObjectManager &	om,
		const string &	dbname = `"nr"`,
		const EDbType	dbtype = `eUnknown`,
		bool	use_fixed_size_slices = `true`,
		CObjectManager::EIsDefault	is_default = `CObjectManager::eNonDefault`,
		CObjectManager::TPriority	priority = `CObjectManager::kPriority_NotSet`
	)

static

◆ RegisterInObjectManager() [3/4]

CBlastDbDataLoader::TRegisterLoaderInfo CBlastDbDataLoader::RegisterInObjectManager	(	CObjectManager &	om,
		CRef< CSeqDB >	db_handle,
		bool	use_fixed_size_slices = `true`,
		CObjectManager::EIsDefault	is_default = `CObjectManager::eNonDefault`,
		CObjectManager::TPriority	priority = `CObjectManager::kPriority_NotSet`
	)

static

Definition at line 67 of file bdbloader.cpp.

References CParamLoaderMaker< TDataLoader, TParam >::GetRegisterInfo(), om, and CDataLoader::RegisterInObjectManager().

◆ RegisterInObjectManager() [4/4]

CBlastDbDataLoader::TRegisterLoaderInfo CBlastDbDataLoader::RegisterInObjectManager	(	CObjectManager &	om,
		CRef< CSeqDB >	db_handle,
		CObjectManager::EIsDefault	is_default = `CObjectManager::eNonDefault`,
		CObjectManager::TPriority	priority = `CObjectManager::kPriority_NotSet`
	)

static

Note: this is added to temporarily comply with the toolkit's stable components rule of having backwards compatible APIs

Definition at line 93 of file bdbloader.cpp.

References om, and RegisterInObjectManager().

◆ x_GetOid() [1/2]

int CBlastDbDataLoader::x_GetOid ( const CSeq_id_Handle & idh )

protected

Gets the OID from m_Ids cache or the BLAST databases.

Definition at line 379 of file bdbloader.cpp.

References _TRACE, CSeq_id::AsFastaString(), CSeq_id::Compare(), CSeq_id::e_YES, limited_size_map< Key, Value, Less >::end(), limited_size_map< Key, Value, Less >::find(), CSeq_id_Handle::GetSeqId(), IBlastDbAdapter::GetSeqIDs(), limited_size_map< Key, Value, Less >::insert(), ITERATE, m_BlastDb, m_Ids, and IBlastDbAdapter::SeqidToOid().

Referenced by GetBlobId(), GetChunk(), and CRemoteBlastDbDataLoader::GetChunks().

◆ x_GetOid() [2/2]

int CBlastDbDataLoader::x_GetOid ( const TBlobId & blob_id ) const

protected

Gets the OID from a TBlobId (see typedef in bdbloader.cpp)

Definition at line 427 of file bdbloader.cpp.

References CBlobIdFor< Value, Converter >::GetValue().

◆ x_LoadData()

void CBlastDbDataLoader::x_LoadData	(	const CSeq_id_Handle &	idh,
		int	oid,
		CTSE_LoadLock &	lock,
		int	slice_size
	)

protected

Load sequence data from cache or from the database.

This checks the OID cache and loads the sequence data from there or if not found, from the CSeqDB database. When new data is built, the sequence is also split into chunks. A description of what data is available will be returned in the "lock" parameter.

Parameters

idh	A handle to the sequence identifier.
oid	Object id in BLAST DB
lock	Information about the sequence data is returned here.

Definition at line 257 of file bdbloader.cpp.

References _ASSERT, CTSE_Split_Info::AddChunk(), CTSE_Info::GetSplitInfo(), CTSE_LoadLock::IsLoaded(), m_BlastDb, m_Ids, m_UseFixedSizeSlices, NON_CONST_ITERATE, CTSE_LoadLock::SetLoaded(), and CTSE_Info::SetSeq_entry().

Referenced by GetBlobById(), and CRemoteBlastDbDataLoader::GetBlobById().

Friends And Related Function Documentation

◆ CParamLoaderMaker< CBlastDbDataLoader, SBlastDbParam >

friend class CParamLoaderMaker< CBlastDbDataLoader, SBlastDbParam >

friend

Definition at line 180 of file bdbloader.hpp.

Member Data Documentation

◆ m_BlastDb

CRef<IBlastDbAdapter> CBlastDbDataLoader::m_BlastDb

protected

The sequence database.

Definition at line 220 of file bdbloader.hpp.

Referenced by CBlastDbDataLoader(), CRemoteBlastDbDataLoader::CRemoteBlastDbDataLoader(), CRemoteBlastDbDataLoader::GetBlobs(), GetChunk(), CRemoteBlastDbDataLoader::GetChunks(), GetSequenceLength(), GetTaxId(), x_GetOid(), and x_LoadData().

◆ m_DBName

string CBlastDbDataLoader::m_DBName

protected

Blast database name.

Definition at line 218 of file bdbloader.hpp.

Referenced by CBlastDbDataLoader(), CRemoteBlastDbDataLoader::CRemoteBlastDbDataLoader(), DebugDump(), and CRemoteBlastDbDataLoader::DebugDump().

◆ m_DBType

EDbType CBlastDbDataLoader::m_DBType

protected

Is this database protein or nucleotide?

Definition at line 219 of file bdbloader.hpp.

Referenced by CBlastDbDataLoader(), CRemoteBlastDbDataLoader::CRemoteBlastDbDataLoader(), DebugDump(), CRemoteBlastDbDataLoader::DebugDump(), GetSequenceType(), and GetSequenceTypes().

◆ m_Ids

TIdMap CBlastDbDataLoader::m_Ids

protected

ID to OID translation.

Definition at line 222 of file bdbloader.hpp.

Referenced by x_GetOid(), and x_LoadData().

◆ m_UseFixedSizeSlices

bool CBlastDbDataLoader::m_UseFixedSizeSlices

protected

Configuration value specified to the CCachedSequence.

Definition at line 225 of file bdbloader.hpp.

Referenced by CRemoteBlastDbDataLoader::CRemoteBlastDbDataLoader(), DebugDump(), CRemoteBlastDbDataLoader::DebugDump(), CBlastDbDataLoader::SBlastDbParam::SBlastDbParam(), and x_LoadData().

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

include/objtools/data_loaders/blastdb/bdbloader.hpp
src/objtools/data_loaders/blastdb/bdbloader.cpp

Classes

Public Types

Public Member Functions

Static Public Member Functions

Protected Types

Protected Member Functions

Protected Attributes

Friends

Additional Inherited Members

Detailed Description

Member Typedef Documentation

◆ TBioseq_setId

◆ TBioseqId

◆ TIdMap

◆ TMaker

◆ TPlace

◆ TRegisterLoaderInfo

Member Enumeration Documentation

◆ EDbType

Constructor & Destructor Documentation

◆ ~CBlastDbDataLoader()

◆ CBlastDbDataLoader() [1/3]

◆ CBlastDbDataLoader() [2/3]

◆ CBlastDbDataLoader() [3/3]

Member Function Documentation

◆ CanGetBlobById()

◆ DebugDump()

◆ GetBlobById()

◆ GetBlobId()

◆ GetChunk()

◆ GetLoaderNameFromArgs() [1/3]

◆ GetLoaderNameFromArgs() [2/3]

◆ GetLoaderNameFromArgs() [3/3]

◆ GetRecords()

◆ GetSequenceLength()

◆ GetSequenceLengths()

◆ GetSequenceType()

◆ GetSequenceTypes()

◆ GetTaxId()

◆ GetTaxIds()

◆ operator=()

◆ RegisterInObjectManager() [1/4]

◆ RegisterInObjectManager() [2/4]

◆ RegisterInObjectManager() [3/4]

◆ RegisterInObjectManager() [4/4]

◆ x_GetOid() [1/2]

◆ x_GetOid() [2/2]

◆ x_LoadData()

Friends And Related Function Documentation

◆ CParamLoaderMaker< CBlastDbDataLoader, SBlastDbParam >

Member Data Documentation

◆ m_BlastDb

◆ m_DBName

◆ m_DBType

◆ m_Ids

◆ m_UseFixedSizeSlices