seqdb_lmdb.cpp File Reference

Implements interface to interact with LMDB files. More...

#include <ncbi_pch.hpp>
#include <objtools/blast/seqdb_reader/impl/seqdb_lmdb.hpp>
#include <objtools/blast/seqdb_reader/impl/seqdbgeneral.hpp>
#include <corelib/ncbifile.hpp>
#include <objects/seqloc/PDB_seq_id.hpp>
#include <cmath>

Include dependency graph for seqdb_lmdb.cpp:

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Classes
struct	SOidSeqIdPair
class	CLookupSeqIds
class	CLookupTaxIds

Macros
#define	SEQDB_LMDB_TIMING
#define	SPEED(time, nentries)   s_FormatNum((size_t)((nentries)/(time)))

Functions
template<class T >
static string	s_FormatNum (T value)
bool	s_CompareIdList (vector< string > &file_idlist, vector< string > &input_idlist)
string	BuildLMDBFileName (const string &basename, bool is_protein, bool use_index, unsigned int index)
	Build the canonical LMDB file name for BLAST databases. More...
string	GetFileNameFromExistingLMDBFile (const string &lmdb_filename, ELMDBFileType file_type)
void	DeleteLMDBFiles (bool db_is_protein, const string &filename)

Detailed Description

Implements interface to interact with LMDB files.

Definition in file seqdb_lmdb.cpp.

Macro Definition Documentation

SEQDB_LMDB_TIMING

#define SEQDB_LMDB_TIMING

Definition at line 42 of file seqdb_lmdb.cpp.

SPEED

#define SPEED	(		time,
			nentries
	)		s_FormatNum((size_t)((nentries)/(time)))

Definition at line 53 of file seqdb_lmdb.cpp.

Function Documentation

BuildLMDBFileName()

string BuildLMDBFileName	(	const string &	basename,
		bool	is_protein,
		bool	use_index = false,
		unsigned int	index = 0
	)

Build the canonical LMDB file name for BLAST databases.

Parameters

basename	Base name of the BLAST database [in]
is_protein	whether the database contains proteins or not [in]

Returns

a file name

Exceptions

std::invalid_argument

in case of empty basename argument

Definition at line 749 of file seqdb_lmdb.cpp.

References basename, kEmptyStr, and NStr::UIntToString().

Referenced by BOOST_AUTO_TEST_CASE(), CWriteDB_Impl::ListFiles(), CBlastdbConvertApp::Run(), s_ConvertV4toV5(), and CWriteDB_Impl::x_Publish().

DeleteLMDBFiles()

void DeleteLMDBFiles	(	bool	db_is_protein,
		const string &	filename
	)

Definition at line 790 of file seqdb_lmdb.cpp.

References f, ITERATE, and SeqDB_GetLMDBFileExtensions().

Referenced by BOOST_AUTO_TEST_CASE().

GetFileNameFromExistingLMDBFile()

string GetFileNameFromExistingLMDBFile	(	const string &	lmdb_filename,
		ELMDBFileType	file_type
	)

Definition at line 763 of file seqdb_lmdb.cpp.

References eLMDB, eOid2SeqIds, eOid2TaxIds, eTaxId2Offsets, eTaxId2Oids, file_type, and NCBI_THROW.

Referenced by BOOST_AUTO_TEST_CASE(), CBlastdbConvertApp::Run(), CWriteDB_LMDB::x_CreateOidToSeqidsLookupFile(), CWriteDB_TaxID::x_CreateOidToTaxIdsLookupFile(), CWriteDB_TaxID::x_CreateTaxIdToOidsLookupFile(), and CWriteDB_Impl::x_Publish().

s_CompareIdList()

bool s_CompareIdList	(	vector< string > &	file_idlist,
		vector< string > &	input_idlist
	)

Definition at line 461 of file seqdb_lmdb.cpp.

References CSeq_id::fParse_AnyLocal, CSeq_id::fParse_PartialOK, CSeq_id::fParse_RawText, CAliasBase< TPrim >::Get(), CPDB_seq_id_Base::GetMol(), CSeq_id_Base::GetPdb(), CSeq_id::GetSeqIdString(), CSeq_id_Base::IsPdb(), and CPDB_seq_id_Base::IsSetChain_id().

Referenced by CSeqDBLMDB::NegativeSeqIdsToOids().

s_FormatNum()

template<class T >

static string s_FormatNum ( T  value )

static

Definition at line 45 of file seqdb_lmdb.cpp.

References locale, and rapidjson::value.