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Showing content from http://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/doxyhtml/tax4blastsqlite_8cpp_source.html below:

NCBI C++ ToolKit: src/objtools/blast/seqdb_reader/tax4blastsqlite.cpp Source File

41 WITH RECURSIVE descendants_from(taxid, parent) AS 44 SELECT T.taxid, T.parent 45 FROM descendants_from D, TaxidInfo T 46 WHERE D.taxid = T.parent) 47 SELECT taxid from descendants_from; 56

oss <<

"Database '"

kFileName

"' not found"

;

80

{

"table"

"TaxidInfo"

81

{

"index"

"TaxidInfoCompositeIdx_parent"

}

83 const string

kSqlStmt =

84 "SELECT COUNT(*) FROM sqlite_master WHERE type=? and name=?;"

;

85 for

(

auto

& [

type

, name] : kRequiredElements) {

91 if

(s->GetInt(0) != 1) {

93

oss <<

"Database '"

m_DbName

"' does not have "

type

;

94

oss <<

" "

<< name <<

". Please run the following command or "

;

95

oss <<

"contact your system administrator to install it:"

<< endl;

96

oss <<

"update_blastdb.pl --decompress taxdb"

;

101

oss <<

"Failed to check for "

type

" "

<< name <<

" in '"

;

111 if

(taxid <= 0)

return

;

123 if

(desc_taxid != taxid)

124

descendants.push_back(desc_taxid);

static const char * kFileName

CNcbiOstrstreamToString class helps convert CNcbiOstrstream to a string Sample usage:

Connection to SQLite database.

int TOperationFlags

Bit mask of EOperationFlags.

@ fExternalMT

Object and all statements and blobs created on top of it will not be used from different threads simu...

@ fJournalOff

Journaling is completely off (not recommended - transactions cannot be rollbacked unless they consist...

@ fSyncOff

Synchronization is off, database can be corrupted on OS crash or power outage.

@ fReadOnly

The DB is read-only. Also forces fVacuumOff flag.

@ fVacuumOff

Vacuuming is off, database file can only grow.

@ fTempToMemory

Mode of storing temporary data.

SQL statement executing on SQLite database.

static const string kDefaultName

Default name for SQLite database (by default installed in $BLASTDB)

void x_SanityCheck()

Simple sanity check to validate the integrity of the database.

unique_ptr< CSQLITE_Statement > m_Statement

Most recent SQLite statement.

virtual void GetLeafNodeTaxids(const int taxid, vector< int > &descendants)

@inheritDoc

string m_DbName

SQLite3 database file name.

virtual ~CTaxonomy4BlastSQLite()

Destructor.

CTaxonomy4BlastSQLite(const string &dbname=kEmptyStr)

Parametrized constructor, uses its arguments to initialize database.

unique_ptr< CSQLITE_Connection > m_DbConn

Connection to SQLite engine.

#define NCBI_THROW(exception_class, err_code, message)

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

#define END_NCBI_SCOPE

End previously defined NCBI scope.

#define BEGIN_NCBI_SCOPE

Define ncbi namespace.

char * dbname(DBPROCESS *dbproc)

Get name of current database.

Defines: CTimeFormat - storage class for time format.

Defines exception class and several constants for SeqDB.

string SeqDB_ResolveDbPath(const string &filename)

Resolve a file path using SeqDB's path algorithms.

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