#include <objtools/blast/seqdb_reader/impl/seqdb_lmdb.hpp>

Inheritance diagram for CSeqDBLMDB:

Collaboration diagram for CSeqDBLMDB:

Public Member Functions
	CSeqDBLMDB (const string &fname)

virtual	~CSeqDBLMDB ()

CSeqDBLMDB &	operator= (const CSeqDBLMDB &)=delete

	CSeqDBLMDB (const CSeqDBLMDB &)=delete

void	GetOids (const vector< string > &accessions, vector< blastdb::TOid > &oids) const
	Get OIDs for a vector of string accessions. More...

void	GetOid (const string &accession, vector< blastdb::TOid > &oids, const bool allow_dup=false) const
	Get OIDs for single string accession. More...

void	GetVolumesInfo (vector< string > &vol_names, vector< blastdb::TOid > &vol_num_oids)
	Return info for all volumes. More...

void	NegativeSeqIdsToOids (const vector< string > &ids, vector< blastdb::TOid > &rv) const
	Get Oids excluded from a vector of input accessions An oid only get exlcuded if all its seqids are found in the input list Note that the order or number of oids returned are independent of the input id list. More...

void	GetOidsForTaxIds (const set< TTaxId > &tax_ids, vector< blastdb::TOid > &oids, vector< TTaxId > &tax_ids_found) const
	Get Oids for Tax Ids list, idenitcal Oids are merged. More...

void	NegativeTaxIdsToOids (const set< TTaxId > &ids, vector< blastdb::TOid > &rv, vector< TTaxId > &tax_ids_found) const
	Get Oids to exclude for Tax ids @parm ids Input tax ids to exclude /Output tax ids found. More...

void	GetDBTaxIds (vector< TTaxId > &tax_ids) const
	Get All Unique Tax Ids for db @parma tax_ids Return all unique tax ids found in db. More...

void	GetTaxIdsForOids (const vector< blastdb::TOid > &oids, set< TTaxId > &tax_ids) const
	Get Tax Ids for oid list. 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 Attributes
string	m_LMDBFile

string	m_Oid2SeqIdsFile

string	m_Oid2TaxIdsFile

string	m_TaxId2OidsFile

string	m_TaxId2OffsetsFile

bool	m_LMDBFileOpened

blastdb::TOid	m_NumOids

Additional Inherited Members
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

Definition at line 43 of file seqdb_lmdb.hpp.

Constructor & Destructor Documentation

◆ CSeqDBLMDB() [1/2]

CSeqDBLMDB::CSeqDBLMDB ( const string & fname )

Definition at line 242 of file seqdb_lmdb.cpp.

◆ ~CSeqDBLMDB()

CSeqDBLMDB::~CSeqDBLMDB ( )

virtual

Definition at line 253 of file seqdb_lmdb.cpp.

References CBlastLMDBManager::CloseEnv(), CBlastLMDBManager::GetInstance(), m_LMDBFile, and m_LMDBFileOpened.

◆ CSeqDBLMDB() [2/2]

CSeqDBLMDB::CSeqDBLMDB ( const CSeqDBLMDB & )

delete

Member Function Documentation

◆ GetDBTaxIds()

void CSeqDBLMDB::GetDBTaxIds ( vector< TTaxId > & tax_ids ) const

Get All Unique Tax Ids for db @parma tax_ids Return all unique tax ids found in db.

Definition at line 558 of file seqdb_lmdb.cpp.

References lmdb::txn::begin(), CBlastLMDBManager::CloseEnv(), lmdb::error::code(), dbname(), env, CSeqDB_Path::FindBaseName(), CBlastLMDBManager::GetInstance(), CBlastLMDBManager::GetReadEnvTax(), CSeqDB_Substring::GetString(), ncbi::grid::netcache::search::fields::key, m_TaxId2OffsetsFile, MDB_NEXT, MDB_NOTFOUND, MDB_RDONLY, NCBI_THROW, lmdb::cursor::open(), and TAX_ID_FROM.

Referenced by CSeqDBLMDBEntry::GetDBTaxIds().

◆ GetOid()

void CSeqDBLMDB::GetOid	(	const string &	accession,
		vector< blastdb::TOid > &	oids,
		const bool	allow_dup = `false`
	)		const

Get OIDs for single string accession.

String accession may have ".version" appended. If there are no matches, oids will be returned empty. If there are multiple matches, and allow_dup is true,

Parameters

accession	String accession (with or without version suffix) [in]
oids	Reference to vector of TOid to receive found OIDs [out]
allow_dup	If true, return all OIDs which match (default false) [in]

Definition at line 262 of file seqdb_lmdb.cpp.

References lmdb::txn::begin(), CBlastLMDBManager::CloseEnv(), lmdb::error::code(), dbname(), env, CSeqDB_Path::FindBaseName(), CBlastLMDBManager::GetInstance(), CBlastLMDBManager::GetReadEnvAcc(), CSeqDB_Substring::GetString(), m_LMDBFile, m_LMDBFileOpened, MDB_GET_CURRENT, MDB_NEXT_DUP, MDB_NOTFOUND, MDB_RDONLY, MDB_SET, NCBI_THROW, lmdb::cursor::open(), and val.

Referenced by CSeqDBLMDBEntry::AccessionToOids().

◆ GetOids()

void CSeqDBLMDB::GetOids	(	const vector< string > &	accessions,
		vector< blastdb::TOid > &	oids
	)		const

Get OIDs for a vector of string accessions.

Accessions may have ".version" appended. Returned vector of OIDs will have the same length as vector of accessions in one-to-one correspondence. Any accessions which are not found will be assigned OIDs of kSeqDBEntryNotFound (-1).

Parameters

accessions	Vector of string accessions [in]
oids	Reference to vector of TOid to receive found OIDs [out]

Definition at line 360 of file seqdb_lmdb.cpp.

References lmdb::txn::begin(), CBlastLMDBManager::CloseEnv(), lmdb::error::code(), dbname(), env, CSeqDB_Path::FindBaseName(), CBlastLMDBManager::GetInstance(), CBlastLMDBManager::GetReadEnvAcc(), CSeqDB_Substring::GetString(), i, kSeqDBEntryNotFound, m_LMDBFile, m_LMDBFileOpened, MDB_GET_CURRENT, MDB_NOTFOUND, MDB_RDONLY, MDB_SET, NCBI_THROW, lmdb::cursor::open(), and val.

Referenced by CSeqDBLMDBEntry::AccessionsToOids(), BOOST_AUTO_TEST_CASE(), and NegativeSeqIdsToOids().

◆ GetOidsForTaxIds()

void CSeqDBLMDB::GetOidsForTaxIds	(	const set< TTaxId > &	tax_ids,
		vector< blastdb::TOid > &	oids,
		vector< TTaxId > &	tax_ids_found
	)		const

Get Oids for Tax Ids list, idenitcal Oids are merged.

Parameters

tax_ids	Input tax ids /Output tax ids found
oids	Oids found for input tax ids

Definition at line 591 of file seqdb_lmdb.cpp.

References lmdb::txn::begin(), CBlastLMDBManager::CloseEnv(), lmdb::error::code(), count, dbname(), env, CSeqDB_Path::FindBaseName(), CBlastLMDBManager::GetInstance(), CMemoryFile::GetPtr(), CBlastLMDBManager::GetReadEnvTax(), CSeqDB_Substring::GetString(), i, ITERATE, log, m_NumOids, m_TaxId2OffsetsFile, m_TaxId2OidsFile, MDB_GET_CURRENT, MDB_NEXT_DUP, MDB_NOTFOUND, MDB_RDONLY, MDB_SET, NCBI_THROW, offsets, lmdb::cursor::open(), ct::sort(), TAX_ID_TO, and val.

Referenced by BOOST_AUTO_TEST_CASE(), NegativeTaxIdsToOids(), and CSeqDBLMDBEntry::TaxIdsToOids().

◆ GetTaxIdsForOids()

void CSeqDBLMDB::GetTaxIdsForOids	(	const vector< blastdb::TOid > &	oids,
		set< TTaxId > &	tax_ids
	)		const

Get Tax Ids for oid list.

Parameters

oids	Input oid list
tax_ids	Output tax id list

Definition at line 737 of file seqdb_lmdb.cpp.

References i, set< Key, Compare >::insert(), lookup(), and m_Oid2TaxIdsFile.

Referenced by CSeqDBLMDBEntry::GetTaxIdsForOids().

◆ GetVolumesInfo()

void CSeqDBLMDB::GetVolumesInfo	(	vector< string > &	vol_names,
		vector< blastdb::TOid > &	vol_num_oids
	)

Return info for all volumes.

Parameters

vol_names	Reference to vector to receive volume names [out]
vol_num_oids	Reference to vector to receive number of OIDs in each volume [out]

Definition at line 306 of file seqdb_lmdb.cpp.

References lmdb::txn::begin(), CBlastLMDBManager::CloseEnv(), lmdb::dbi_stat(), env, CBlastLMDBManager::GetInstance(), CBlastLMDBManager::GetReadEnvVol(), i, m_LMDBFile, m_NumOids, MDB_GET_CURRENT, MDB_RDONLY, MDB_SET, MDB_stat::ms_entries, NCBI_THROW, lmdb::cursor::open(), and val.

Referenced by BOOST_AUTO_TEST_CASE(), and CSeqDBLMDBEntry::CSeqDBLMDBEntry().

◆ NegativeSeqIdsToOids()

void CSeqDBLMDB::NegativeSeqIdsToOids	(	const vector< string > &	ids,
		vector< blastdb::TOid > &	rv
	)		const

Get Oids excluded from a vector of input accessions An oid only get exlcuded if all its seqids are found in the input list Note that the order or number of oids returned are independent of the input id list.

Parameters

ids	Accessions to exclude
rv	Oids that are excluded

Definition at line 515 of file seqdb_lmdb.cpp.

References SOidSeqIdPair::cmp_oid(), GetOids(), i, kSeqDBEntryNotFound, lookup(), m_Oid2SeqIdsFile, s_CompareIdList(), and ct::sort().

Referenced by BOOST_AUTO_TEST_CASE(), and CSeqDBLMDBEntry::NegativeSeqIdsToOids().

◆ NegativeTaxIdsToOids()

void CSeqDBLMDB::NegativeTaxIdsToOids	(	const set< TTaxId > &	ids,
		vector< blastdb::TOid > &	rv,
		vector< TTaxId > &	tax_ids_found
	)		const

Get Oids to exclude for Tax ids @parm ids Input tax ids to exclude /Output tax ids found.

Parameters

rv	Oids to exclude based on input tax id list

Definition at line 709 of file seqdb_lmdb.cpp.

References set< Key, Compare >::end(), set< Key, Compare >::find(), GetOidsForTaxIds(), i, lookup(), m_Oid2TaxIdsFile, and set< Key, Compare >::size().

Referenced by BOOST_AUTO_TEST_CASE(), and CSeqDBLMDBEntry::NegativeTaxIdsToOids().

◆ operator=()

CSeqDBLMDB& CSeqDBLMDB::operator= ( const CSeqDBLMDB & )

delete

Member Data Documentation

◆ m_LMDBFile

string CSeqDBLMDB::m_LMDBFile

private

Definition at line 103 of file seqdb_lmdb.hpp.

Referenced by GetOid(), GetOids(), GetVolumesInfo(), and ~CSeqDBLMDB().

◆ m_LMDBFileOpened

bool CSeqDBLMDB::m_LMDBFileOpened

mutableprivate

Definition at line 108 of file seqdb_lmdb.hpp.

Referenced by GetOid(), GetOids(), and ~CSeqDBLMDB().

◆ m_NumOids

blastdb::TOid CSeqDBLMDB::m_NumOids

private

Definition at line 109 of file seqdb_lmdb.hpp.

Referenced by GetOidsForTaxIds(), and GetVolumesInfo().

◆ m_Oid2SeqIdsFile

string CSeqDBLMDB::m_Oid2SeqIdsFile

private

Definition at line 104 of file seqdb_lmdb.hpp.

Referenced by NegativeSeqIdsToOids().

◆ m_Oid2TaxIdsFile

string CSeqDBLMDB::m_Oid2TaxIdsFile

private

Definition at line 105 of file seqdb_lmdb.hpp.

Referenced by GetTaxIdsForOids(), and NegativeTaxIdsToOids().

◆ m_TaxId2OffsetsFile

string CSeqDBLMDB::m_TaxId2OffsetsFile

private

Definition at line 107 of file seqdb_lmdb.hpp.

Referenced by GetDBTaxIds(), and GetOidsForTaxIds().

◆ m_TaxId2OidsFile

string CSeqDBLMDB::m_TaxId2OidsFile

private

Definition at line 106 of file seqdb_lmdb.hpp.

Referenced by GetOidsForTaxIds().

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

include/objtools/blast/seqdb_reader/impl/seqdb_lmdb.hpp
src/objtools/blast/seqdb_reader/seqdb_lmdb.cpp

Public Member Functions

Private Attributes

Additional Inherited Members

Detailed Description

Constructor & Destructor Documentation

◆ CSeqDBLMDB() [1/2]

◆ ~CSeqDBLMDB()

◆ CSeqDBLMDB() [2/2]

Member Function Documentation

◆ GetDBTaxIds()

◆ GetOid()

◆ GetOids()

◆ GetOidsForTaxIds()

◆ GetTaxIdsForOids()

◆ GetVolumesInfo()

◆ NegativeSeqIdsToOids()

◆ NegativeTaxIdsToOids()

◆ operator=()

Member Data Documentation

◆ m_LMDBFile

◆ m_LMDBFileOpened

◆ m_NumOids

◆ m_Oid2SeqIdsFile

◆ m_Oid2TaxIdsFile

◆ m_TaxId2OffsetsFile

◆ m_TaxId2OidsFile