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

m_OIDStart (start_oid),

vector<string> tmp_name;

vector<TOid> tmp_num_oids;

total_num_oids_lmdb = 0;

vector<string>::const_iterator itr = vol_names.begin();

(vol_names.size() > tmp_name.size()) {

(

=0;

< tmp_name.size();

++) {

total_num_oids_lmdb += tmp_num_oids[

];

v.

= total_num_oids_lmdb;

((itr != vol_names.end()) && (*itr == v.

)) {

(

!= total_num_oids_lmdb) {

(

=0;

< oids.size();

++) {

(

=0;

< oids.size();

++) {

skipped_oids = 0;

(

j=0;j <

.size(); j++) {

skipped_oids +=

[j].skipped_oids;

(

=0;

< oids.size();

++) {

(

=0;

< oids.size();

++) {

skipped_oids = 0;

(

j=0;j <

.size(); j++) {

skipped_oids +=

[j].skipped_oids;

skipped_oids = 0;

(

=0;

< oids.size();

++) {

skipped_oids +=

[j].skipped_oids;

.push_back(oids[

] + skipped_oids) ;

vector<string> lmdb_vol_names;

version5 =

;

(version5 ==

) {

vol_lmdb_full_name;

lmdb_full_name = vol_lmdb_full_name;

(vol_lmdb_full_name == lmdb_full_name) {

lmdb_vol_names.push_back(vol_name);

lmdb_vol_names.clear();

(entry->GetOIDEnd() < 0) {

lmdb_full_name = vol_lmdb_full_name;

lmdb_vol_names.push_back(vol_name);

lmdb_vol_names.clear();

(entry->GetOIDEnd() < 0) {

oids.insert(oids.end(),

.begin(),

.end());

vector <TOid>

(accs.size(), 0);

(

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

vector <TOid>

(ids.size(), 0);

rv.insert(rv.end(),

.begin(),

.end());

vector<TTaxId> tax_ids_found;

rv_tax_ids.

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

rv.insert(rv.end(),

.begin(),

.end());

(rv_tax_ids.

() < tax_ids.

()) {

rv_tax_ids.

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

(rv.size() == 0) {

tax_ids.

(rv_tax_ids);

vector<TTaxId> tax_ids_found;

[0]->NegativeTaxIdsToOids(tax_ids, rv, tax_ids_found);

rv_tax_ids.

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

rv.insert(rv.end(),

.begin(),

.end());

(rv_tax_ids.

() < tax_ids.

()) {

rv_tax_ids.

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

(rv.size() == 0) {

tax_ids.

(rv_tax_ids);

tax_ids.

(

.begin(),

.end());

tax_ids.

(

.begin(),

.end());

(

=0;

< oids.size();

++){

actual_db_list;

short_name , dir_part, out_name;

( with_dir_path ) {

out_name = dir_part + short_name ;

out_name = short_name;

( !actual_db_list.empty() ) actual_db_list.append(

);

actual_db_list.append( out_name ) ;

actual_db_list ;

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

void x_AdjustOidsOffset(vector< TOid > &oids) const

void GetDBTaxIds(vector< TTaxId > &tax_ids) const

CSeqDBLMDBEntry(const string &name, TOid start_oid, const vector< string > &vol_names)

Constructor.

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

void AccessionsToOids(const vector< string > &accs, vector< TOid > &oids) const

void TaxIdsToOids(const set< TTaxId > &tax_ids, vector< blastdb::TOid > &rv, vector< TTaxId > &tax_ids_found) const

void x_AdjustOidsOffset_TaxList(vector< TOid > &oids) const

TOid m_OIDEnd

The end of the OID range.

TOid m_OIDStart

The start of the OID range.

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

void AccessionToOids(const string &acc, vector< TOid > &oids) const

vector< SVolumeInfo > m_VolInfo

CRef< CSeqDBLMDB > m_LMDB

The underlying volume object.

CSeqDBLMDBSet()

Default Constructor.

vector< CRef< CSeqDBLMDBEntry > > m_LMDBEntrySet

void AccessionToOids(const string &acc, vector< TOid > &oids) const

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

std::string GetDBFileNames(bool with_dir_path=false) const

~CSeqDBLMDBSet()

Destructor.

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

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

void GetLMDBFileNames(vector< string > &lmdb_list) const

void AccessionsToOids(const vector< string > &accs, vector< TOid > &oids) const

void GetDBTaxIds(set< TTaxId > &tax_ids) const

void TaxIdsToOids(set< TTaxId > &tax_ids, vector< blastdb::TOid > &rv) const

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.

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

Get Tax Ids for oid list.

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.

const CSeqDBVol * GetVol(int i) const

Find a volume by index.

int GetNumVols() const

Get the number of volumes.

const string & GetVolName() const

Get the volume name.

string GetLMDBFileName() const

Get sqlite file name associated with this volume Empty string if version 4.

CSeqDB_Substring FindDirName() const

Returns the portion of this path containing the directory.

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.

iterator_bool insert(const value_type &val)

const_iterator begin() const

const_iterator end() const

#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 Warning(CExceptionArgs_Base &args)

static void SplitPath(const string &path, string *dir=0, string *base=0, string *ext=0)

Split a path string into its basic components.

void Reset(void)

Reset reference object.

#define END_NCBI_SCOPE

End previously defined NCBI scope.

#define BEGIN_NCBI_SCOPE

Define ncbi namespace.

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

const blastdb::TOid kSeqDBEntryNotFound

void SeqDB_CombinePath(const CSeqDB_Substring &path, const CSeqDB_Substring &file, const CSeqDB_Substring *extn, string &outp)

Combine a filesystem path and file name.

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