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Showing content from http://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/doxyhtml/seqdb__lmdb_8cpp_source.html below:

NCBI C++ ToolKit: src/objtools/blast/seqdb_reader/seqdb_lmdb.cpp Source File

oss << std::fixed <<

;

m_Filename(fname), m_FileType(

),m_Env(

::

::create()), m_Count(1), m_ReadOnly(read_only)

(

, eFileErr,

+ fname +

);

(

=0;

< m_dbis.size();

++){

(m_dbis[

] != UINT_MAX) {

(m_dbis[dbi_type] == UINT_MAX) {

err =

;

err +=

;

eDbiTaxid2offset:

err +=

;

m_dbis[dbi_type];

m_Env.set_mapsize(map_size);

lmdb_manager.

();

((*itr)->GetFilename() == fname) {

(*itr)->AddReference();

( opened && !*opened ) {

(*itr)->AddReference();

( opened && !*opened ) {

((*itr)->GetFilename() == fname) {

(*itr)->AddReference();

(*itr)->GetEnv();

((*itr)->GetFilename() == fname) {

((*itr)->RemoveReference() == 0) {

m_LMDBFileOpened(

),

(

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

allow_dup)

acc = accession;

(cursor.get(data2find,

)) {

* d =

.data();

oids.push_back(((d[3] << 24)&0xFF000000) | ((d[2] << 16) & 0xFF0000) | ((d[1] << 8) & 0xFF00) | (d[0]&0xFF));

oids.push_back(((d[3] << 24)&0xFF000000) | ((d[2] << 16) & 0xFF0000) | ((d[1] << 8) & 0xFF00) | (d[0]&0xFF));

vol_num_oids.clear();

volinfo_stat, volname_stat;

vol_num_oids.resize(volinfo_stat.

);

(

=0;

< volinfo_stat.

;

++) {

(cursor_volname.get(data2find,

)) {

vol_names[

].assign(

.data(),

.size());

(cursor_volinfo.get(data2find,

)) {

* d =

.data();

vol_num_oids[

] = (((d[3] << 24)&0xFF000000) | ((d[2] << 16) & 0xFF0000) | ((d[1] << 8) & 0xFF00) | (d[0]&0xFF));

cursor_volname.close();

cursor_volinfo.close();

(

j=0; j < vol_num_oids.size(); j++){

(

=0;

< accessions.size();

++) {

acc = accessions[

];

(cursor.get(data2find,

)) {

* d =

.data();

oids[

] = (((d[3] << 24)&0xFF000000) | ((d[2] << 16) & 0xFF0000) | ((d[1] << 8) & 0xFF00) | (d[0]&0xFF));

(v.

< k.

);

(v.

< k.

);

(begin < end) {

id_len = *begin;

(id_len == 0xFF) {

.assign(begin, long_id_len);

begin += long_id_len;

idlist.push_back(

);

.assign(begin, id_len);

idlist.push_back(

);

vector<string>::iterator f_itr = file_idlist.begin();

vector<string>::iterator i_itr = input_idlist.begin();

(f_itr != file_idlist.end() && i_itr != input_idlist.end()) {

(*i_itr == *f_itr) {

tmp_pdb = *i_itr;

((f_itr != file_idlist.end()) && ((*f_itr).find_first_of(tmp_pdb) == 0)){

((i_itr != input_idlist.end()) && ((*i_itr).find_first_of(tmp_pdb) == 0)){

((i_itr != input_idlist.end()) && (file_seq_id.

(

) == *i_itr)){

(f_itr == file_idlist.end()){

input_idlist.clear();

vector<blastdb::TOid> oids;

vector<SOidSeqIdPair> pairs;

(

=0;

< ids.size();

++) {

(pairs.size() == 0) {

(

< pairs.size()) {

vector<string> file_idlist;

vector<string> input_idlist;

current_oid = pairs[

].oid;

.GetSeqIdListForOid(current_oid, file_idlist);

((

< pairs.size()) && (current_oid == pairs[

].oid)) {

input_idlist.push_back(pairs[

].

);

rv.push_back(current_oid);

dbi(dbi_handle);

tax_ids.push_back(taxid);

tax_ids_found.clear();

(cursor.get(data2find,

)) {

* d =

.data();

.push_back((((

) d[7] << 56) &0xFF00000000000000) | (((

) d[6] << 48) & 0xFF000000000000) |

(((

) d[5] << 40) &0xFF0000000000) | (((

) d[4] << 32) & 0xFF00000000) |

(((

) d[3] << 24) &0xFF000000) | (((

) d[2] << 16) & 0xFF0000) |

(((

) d[1] << 8) &0xFF00) | ((

) d[0]&0xFF));

.push_back((((

) d[7] << 56) &0xFF00000000000000) | (((

) d[6] << 48) & 0xFF000000000000) |

(((

) d[5] << 40) &0xFF0000000000) | (((

) d[4] << 32) & 0xFF00000000) |

(((

) d[3] << 24) &0xFF000000) | (((

) d[2] << 16) & 0xFF0000) |

(((

) d[1] << 8) &0xFF00) | ((

) d[0]&0xFF));

tax_ids_found.push_back(*itr);

vector<bool> oids_set(

,

);

* start_ptr = (

*) oid_file.

();

(

=0;

<

.size();

++) {

num_of_oids = *list_ptr;

(

< num_of_oids) {

(!oids_set[*list_ptr]) {

oids.push_back(*list_ptr);

oids_set[*list_ptr] =

;

oids_sz = oids.size();

(oids.begin(), oids.end());

oids.reserve(oids_sz);

(

=0;

< oids_set.size();

++) {

(begin < end) {

vector<blastdb::TOid> oids;

tax_id_list(tax_ids_found.begin(), tax_ids_found.end());

(

=0;

< oids.size();

++) {

vector<TTaxId> file_list;

.GetTaxIdListForOid(oids[

], file_list);

(file_list.size() > tax_ids.

()) {

(; j < file_list.size(); j++) {

(tax_id_list.

(file_list[j]) == tax_id_list.

()) {

(j == file_list.size()) {

rv.push_back(oids[

]);

(

=0;

< oids.size();

++) {

vector<TTaxId> taxid_list;

.GetTaxIdListForOid(oids[

], taxid_list);

tax_ids.

(taxid_list.begin(), taxid_list.end());

invalid_argument(

);

vol_str = (index > 9) ?

:

;

+ vol_str + (is_protein ?

:

);

filename (lmdb_filename, 0, lmdb_filename.size() - 2);

(vector<string>, itr, extn) {

(filename +

+ (*itr));

unsigned int AddReference()

MDB_dbi GetDbi(EDbiType dbi_type)

void SetMapSize(Uint8 map_size)

void InitDbi(lmdb::env &env, ELMDBFileType file_type)

CBlastEnv(const string &fname, ELMDBFileType file_type, bool read_only=true, Uint8 map_size=0)

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

static CBlastLMDBManager & GetInstance()

lmdb::env & GetWriteEnv(const string &fname, Uint8 map_size)

lmdb::env & GetReadEnvAcc(const string &fname, MDB_dbi &db_acc, bool *opened=0)

list< CBlastEnv * > m_EnvList

lmdb::env & GetReadEnvTax(const string &fname, MDB_dbi &db_tax, bool *opened=0)

void CloseEnv(const string &fname)

CBlastEnv * GetBlastEnv(const string &fname, ELMDBFileType file_type, bool *opened=0)

lmdb::env & GetReadEnvVol(const string &fname, MDB_dbi &db_volname, MDB_dbi &db_volinfo)

void GetSeqIdListForOid(blastdb::TOid oid, vector< string > &idlist)

CLookupSeqIds(CMemoryFile &file)

void GetTaxIdListForOid(blastdb::TOid oid, vector< TTaxId > &taxid_list)

CLookupTaxIds(CMemoryFile &file)

CNcbiOstrstreamToString class helps convert CNcbiOstrstream to a string Sample usage:

T & Get(void)

Create the variable if not created yet, return the reference.

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

Get OIDs for a vector of string accessions.

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

Get OIDs for single string accession.

string m_TaxId2OffsetsFile

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

Get Tax Ids for oid list.

CSeqDBLMDB(const string &fname)

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.

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 fo...

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.

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

Return info for all volumes.

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.

CSeqDB_Substring FindBaseName() const

Returns the portion of this path containing the base name.

void GetString(string &s) const

Return the data by assigning it to a string.

static cursor open(MDB_txn *const txn, const MDB_dbi dbi)

Creates an LMDB cursor.

Resource class for `MDB_dbi` handles.

static dbi open(MDB_txn *const txn, const char *const name=nullptr, const unsigned int flags=default_flags)

Opens a database handle.

MDB_dbi handle() const noexcept

Returns the underlying `MDB_dbi` handle.

Resource class for `MDB_env*` handles.

env & open(const char *const path, const unsigned int flags=default_flags, const mode mode=default_mode)

Opens this environment.

env & set_max_dbs(const MDB_dbi count)

env & set_mapsize(const std::size_t size)

Base class for LMDB exception conditions.

virtual const char * what() const noexcept

Returns the underlying LMDB error code.

int code() const noexcept

Returns the underlying LMDB error code.

static txn begin(MDB_env *const env, MDB_txn *const parent=nullptr, const unsigned int flags=default_flags)

Creates a new LMDB transaction.

Wrapper class for `MDB_val` structures.

iterator_bool insert(const value_type &val)

const_iterator find(const key_type &key) const

const_iterator end() const

static int lookup(const char *name, const struct lookup_int *table)

#define ITERATE(Type, Var, Cont)

ITERATE macro to sequence through container elements.

#define TAX_ID_TO(T, tax_id)

#define NON_CONST_ITERATE(Type, Var, Cont)

Non constant version of ITERATE macro.

SStrictId_Tax::TId TTaxId

Taxon id type.

#define TAX_ID_FROM(T, value)

#define LOG_POST(message)

This macro is deprecated and it's strongly recomended to move in all projects (except tests) to macro...

#define NCBI_THROW(exception_class, err_code, message)

Generic macro to throw an exception, given the exception class, error code and message string.

void Info(CExceptionArgs_Base &args)

Int8 GetLength(void) const

Get size of file.

void * GetPtr(void) const

Get pointer to beginning of data.

virtual bool Exists(void) const

Check existence of file.

const TPrim & Get(void) const

string GetSeqIdString(bool with_version=false) const

Return seqid string with optional version for text seqid type.

@ fParse_RawText

Try to ID raw non-numeric accessions.

@ fParse_PartialOK

Warn rather than throwing an exception when a FASTA-style ID set contains unparsable portions,...

@ fParse_AnyLocal

Treat otherwise unidentified strings as local accessions as long as they don't resemble FASTA-style I...

int32_t Int4

4-byte (32-bit) signed integer

char Char

Alias for char.

uint32_t Uint4

4-byte (32-bit) unsigned integer

uint64_t Uint8

8-byte (64-bit) unsigned integer

#define END_NCBI_SCOPE

End previously defined NCBI scope.

#define BEGIN_NCBI_SCOPE

Define ncbi namespace.

static string UIntToString(unsigned int value, TNumToStringFlags flags=0, int base=10)

Convert UInt to string.

const TPdb & GetPdb(void) const

Get the variant data.

bool IsSetChain_id(void) const

chain identifier; length-independent generalization of 'chain' Check if a value has been assigned to ...

bool IsPdb(void) const

Check if variant Pdb is selected.

const TMol & GetMol(void) const

Get the Mol member data.

char * dbname(DBPROCESS *dbproc)

Get name of current database.

#define MDB_NOTFOUND

key/data pair not found (EOF)

void mdb_dbi_close(MDB_env *env, MDB_dbi dbi)

Close a database handle.

@ MDB_SET

Position at specified key.

@ MDB_NEXT_DUP

Position at next data item of current key.

@ MDB_NEXT

Position at next data item.

@ MDB_GET_CURRENT

Return key/data at current cursor position.

#define MDB_INTEGERKEY

numeric keys in native byte order: either unsigned int or size_t.

#define MDB_DUPFIXED

with MDB_DUPSORT, sorted dup items have fixed size

#define MDB_DUPSORT

use sorted duplicates

#define MDB_NOLOCK

don't do any locking, caller must manage their own locks

#define MDB_NOSUBDIR

no environment directory

#define MDB_RDONLY

read only

size_t ms_entries

Number of data items.

unsigned int MDB_dbi

A handle for an individual database in the DB environment.

constexpr auto sort(_Init &&init)

static void dbi_stat(MDB_txn *txn, MDB_dbi dbi, MDB_stat *stat)

const struct ncbi::grid::netcache::search::fields::KEY key

const GenericPointer< typename T::ValueType > T2 value

Defines classes: CDirEntry, CFile, CDir, CSymLink, CMemoryFile, CFileUtil, CFileLock,...

static const char * locale

static PCRE2_SIZE * offsets

void DeleteLMDBFiles(bool db_is_protein, const string &filename)

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

Build the canonical LMDB file name for BLAST databases.

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

static string s_FormatNum(T value)

string GetFileNameFromExistingLMDBFile(const string &lmdb_filename, ELMDBFileType file_type)

Defines interface to interact with LMDB files.

const string taxid2offset_str

void SeqDB_GetLMDBFileExtensions(bool db_is_protein, vector< string > &extn)

Retrieves file extensions for BLAST LMDB files.

const blastdb::TOid kSeqDBEntryNotFound

Int4 TOid

Ordinal ID in BLAST databases.

This file defines several SeqDB utility functions related to byte order and file system portability.

Statistics for a database in the environment.

SOidSeqIdPair(blastdb::TOid o, const string &i)

static bool cmp_oid(const SOidSeqIdPair &v, const SOidSeqIdPair &k)

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