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Showing content from http://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/doxyhtml/seqdb__lmdb_8hpp_source.html below:

NCBI C++ ToolKit: include/objtools/blast/seqdb_reader/impl/seqdb_lmdb.hpp Source File

1 #ifndef OBJTOOLS_READERS_BLAST__SEQDB__SEQDB_LMDB_HPP 2 #define OBJTOOLS_READERS_BLAST__SEQDB__SEQDB_LMDB_HPP 59 void

GetOids(

const

vector<string>& accessions, vector<blastdb::TOid>& oids)

const

;

68 void

GetOid(

const string

& accession, vector<blastdb::TOid>& oids,

const bool

allow_dup =

false

)

const

;

74 void

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

81 void

NegativeSeqIdsToOids(

const

vector<string>& ids, vector<blastdb::TOid>& rv)

const

;

86 void

GetOidsForTaxIds(

const set<TTaxId>

& tax_ids, vector<blastdb::TOid>& oids, vector<TTaxId> & tax_ids_found)

const

;

91 void

NegativeTaxIdsToOids(

const set<TTaxId>

& ids, vector<blastdb::TOid>& rv, vector<TTaxId> & tax_ids_found)

const

;

95 void

GetDBTaxIds(vector<TTaxId> & tax_ids)

const

;

100 void

GetTaxIdsForOids(

const

vector<blastdb::TOid> & oids,

set<TTaxId>

& tax_ids)

const

;

134 void DeleteLMDBFiles

(

bool

db_is_protein,

const string

& lmdb_filename);

143 lmdb::env

& GetReadEnvAcc(

const string

& fname,

MDB_dbi

& db_acc,

bool

* opened = 0);

144 lmdb::env

& GetReadEnvTax(

const string

& fname,

MDB_dbi

& db_tax,

bool

* opened = 0);

147 void

CloseEnv(

const string

& fname);

166 MDB_dbi

GetDbi(EDbiType dbi_type);

168 void

SetMapSize(

Uint8

map_size);

192 typename

vector<V>::iterator itr = std::unique(

.begin(),

.end());

193 a

.resize(std::distance(

.begin(), itr));

unsigned int AddReference()

const string & GetFilename() const

unsigned int RemoveReference()

Class for manageing LMDB env, each env should only be open once.

list< CBlastEnv * > m_EnvList

Helper class for object allocation/deallocation.

CSeqDBLMDB & operator=(const CSeqDBLMDB &)=delete

string m_TaxId2OffsetsFile

CSeqDBLMDB(const CSeqDBLMDB &)=delete

Resource class for `MDB_env*` handles.

uint64_t Uint8

8-byte (64-bit) unsigned integer

#define END_NCBI_SCOPE

End previously defined NCBI scope.

#define END_SCOPE(ns)

End the previously defined scope.

#define BEGIN_NCBI_SCOPE

Define ncbi namespace.

#define BEGIN_SCOPE(ns)

Define a new scope.

#define NCBI_XOBJREAD_EXPORT

unsigned int MDB_dbi

A handle for an individual database in the DB environment.

constexpr auto sort(_Init &&init)

Static variables safety - create on demand, destroy on application termination.

const string taxid2offset_str

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.

void DeleteLMDBFiles(bool db_is_protein, const string &lmdb_filename)

string GetFileNameFromExistingLMDBFile(const string &lmdb_filename, ELMDBFileType file_type)

void SortAndUnique(vector< V > &a)

Defines exception class and several constants for SeqDB.

Int4 TOid

Ordinal ID in BLAST databases.

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