NCBI C++ ToolKit
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CTaxonomy4BlastSQLite Class Reference

Search Toolkit Book for CTaxonomy4BlastSQLite

Clas to retrieve taxonomic information for filtering BLASTDBs. More...

#include <objtools/blast/seqdb_reader/tax4blastsqlite.hpp>

+ Inheritance diagram for CTaxonomy4BlastSQLite:
+ Collaboration diagram for CTaxonomy4BlastSQLite:

Public Member Functions

 CTaxonomy4BlastSQLite (const string &dbname=kEmptyStr)
 Parametrized constructor, uses its arguments to initialize database. More...
 
virtual ~CTaxonomy4BlastSQLite ()
 Destructor. More...
 
virtual void GetLeafNodeTaxids (const int taxid, vector< int > &descendants)
 @inheritDoc More...
 
 CTaxonomy4BlastSQLite (const CTaxonomy4BlastSQLite &)=delete
 
CTaxonomy4BlastSQLiteoperator= (const CTaxonomy4BlastSQLite &)=delete
 
- Public Member Functions inherited from CObject
 CObject (void)
 Constructor. More...
 
 CObject (const CObject &src)
 Copy constructor. More...
 
virtual ~CObject (void)
 Destructor. More...
 
CObjectoperator= (const CObject &src) THROWS_NONE
 Assignment operator. More...
 
bool CanBeDeleted (void) const THROWS_NONE
 Check if object can be deleted. More...
 
bool IsAllocatedInPool (void) const THROWS_NONE
 Check if object is allocated in memory pool (not system heap) More...
 
bool Referenced (void) const THROWS_NONE
 Check if object is referenced. More...
 
bool ReferencedOnlyOnce (void) const THROWS_NONE
 Check if object is referenced only once. More...
 
void AddReference (void) const
 Add reference to object. More...
 
void RemoveReference (void) const
 Remove reference to object. More...
 
void ReleaseReference (void) const
 Remove reference without deleting object. More...
 
virtual void DoNotDeleteThisObject (void)
 Mark this object as not allocated in heap – do not delete this object. More...
 
virtual void DoDeleteThisObject (void)
 Mark this object as allocated in heap – object can be deleted. More...
 
void * operator new (size_t size)
 Define new operator for memory allocation. More...
 
void * operator new[] (size_t size)
 Define new[] operator for 'array' memory allocation. More...
 
void operator delete (void *ptr)
 Define delete operator for memory deallocation. More...
 
void operator delete[] (void *ptr)
 Define delete[] operator for memory deallocation. More...
 
void * operator new (size_t size, void *place)
 Define new operator. More...
 
void operator delete (void *ptr, void *place)
 Define delete operator. More...
 
void * operator new (size_t size, CObjectMemoryPool *place)
 Define new operator using memory pool. More...
 
void operator delete (void *ptr, CObjectMemoryPool *place)
 Define delete operator. More...
 
virtual void DebugDump (CDebugDumpContext ddc, unsigned int depth) const
 Define method for dumping debug information. More...
 
- Public Member Functions inherited from CDebugDumpable
 CDebugDumpable (void)
 
virtual ~CDebugDumpable (void)
 
void DebugDumpText (ostream &out, const string &bundle, unsigned int depth) const
 
void DebugDumpFormat (CDebugDumpFormatter &ddf, const string &bundle, unsigned int depth) const
 
void DumpToConsole (void) const
 

Static Public Attributes

static const string kDefaultName
 Default name for SQLite database (by default installed in $BLASTDB) More...
 
- Static Public Attributes inherited from CObject
static const TCount eCounterBitsCanBeDeleted = 1 << 0
 Define possible object states. More...
 
static const TCount eCounterBitsInPlainHeap = 1 << 1
 Heap signature was found. More...
 
static const TCount eCounterBitsPlaceMask
 Mask for 'in heap' state flags. More...
 
static const int eCounterStep = 1 << 2
 Skip over the "in heap" bits. More...
 
static const TCount eCounterValid = TCount(1) << (sizeof(TCount) * 8 - 2)
 Minimal value for valid objects (reference counter is zero) Must be a single bit value. More...
 
static const TCount eCounterStateMask
 Valid object, and object in heap. More...
 

Private Member Functions

void x_SanityCheck ()
 Simple sanity check to validate the integrity of the database. More...
 

Private Attributes

string m_DbName
 SQLite3 database file name. More...
 
unique_ptr< CSQLITE_Statementm_Statement
 Most recent SQLite statement. More...
 
unique_ptr< CSQLITE_Connectionm_DbConn
 Connection to SQLite engine. More...
 

Additional Inherited Members

- Public Types inherited from CObject
enum  EAllocFillMode { eAllocFillNone = 1 , eAllocFillZero , eAllocFillPattern }
 Control filling of newly allocated memory. More...
 
typedef CObjectCounterLocker TLockerType
 Default locker type for CRef. More...
 
typedef atomic< Uint8TCounter
 Counter type is CAtomiCounter. More...
 
typedef Uint8 TCount
 Alias for value type of counter. More...
 
- Static Public Member Functions inherited from CObject
static NCBI_XNCBI_EXPORT void ThrowNullPointerException (void)
 Define method to throw null pointer exception. More...
 
static NCBI_XNCBI_EXPORT void ThrowNullPointerException (const type_info &type)
 
static EAllocFillMode GetAllocFillMode (void)
 
static void SetAllocFillMode (EAllocFillMode mode)
 
static void SetAllocFillMode (const string &value)
 Set mode from configuration parameter value. More...
 
- Static Public Member Functions inherited from CDebugDumpable
static void EnableDebugDump (bool on)
 
- Protected Member Functions inherited from CObject
virtual void DeleteThis (void)
 Virtual method "deleting" this object. More...
 

Detailed Description

Clas to retrieve taxonomic information for filtering BLASTDBs.

Definition at line 42 of file tax4blastsqlite.hpp.

Constructor & Destructor Documentation

◆ CTaxonomy4BlastSQLite() [1/2]

CTaxonomy4BlastSQLite::CTaxonomy4BlastSQLite ( const string dbname = kEmptyStr)

Parametrized constructor, uses its arguments to initialize database.

Parameters
dbnamebase name of the database file. If not provided, kDefaultName is used [in]
Exceptions
CSeqDBExceptionif the database file is not found or appears invalid

Definition at line 54 of file tax4blastsqlite.cpp.

References dbname(), CSQLITE_Connection::fExternalMT, CSQLITE_Connection::fJournalOff, CSQLITE_Connection::fReadOnly, CSQLITE_Connection::fSyncOff, CSQLITE_Connection::fTempToMemory, CSQLITE_Connection::fVacuumOff, kDefaultName, kFileName, m_DbConn, m_DbName, NCBI_THROW, SeqDB_ResolveDbPath(), and x_SanityCheck().

◆ ~CTaxonomy4BlastSQLite()

CTaxonomy4BlastSQLite::~CTaxonomy4BlastSQLite ( )
virtual

Destructor.

Definition at line 75 of file tax4blastsqlite.cpp.

References m_DbConn, and m_Statement.

◆ CTaxonomy4BlastSQLite() [2/2]

CTaxonomy4BlastSQLite::CTaxonomy4BlastSQLite ( const CTaxonomy4BlastSQLite )
delete

Member Function Documentation

◆ GetLeafNodeTaxids()

void CTaxonomy4BlastSQLite::GetLeafNodeTaxids ( const int  taxid,
vector< int > &  descendants 
)
virtual

@inheritDoc

Implements ITaxonomy4Blast.

Definition at line 112 of file tax4blastsqlite.cpp.

References kSQLQuery, m_DbConn, and m_Statement.

◆ operator=()

CTaxonomy4BlastSQLite& CTaxonomy4BlastSQLite::operator= ( const CTaxonomy4BlastSQLite )
delete

◆ x_SanityCheck()

void CTaxonomy4BlastSQLite::x_SanityCheck ( )
private

Simple sanity check to validate the integrity of the database.

Definition at line 81 of file tax4blastsqlite.cpp.

References m_DbConn, m_DbName, NCBI_THROW, and type.

Referenced by CTaxonomy4BlastSQLite().

Member Data Documentation

◆ kDefaultName

const string CTaxonomy4BlastSQLite::kDefaultName
static

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

Definition at line 47 of file tax4blastsqlite.hpp.

Referenced by CTaxonomy4BlastSQLite().

◆ m_DbConn

unique_ptr<CSQLITE_Connection> CTaxonomy4BlastSQLite::m_DbConn
private

Connection to SQLite engine.

Definition at line 74 of file tax4blastsqlite.hpp.

Referenced by CTaxonomy4BlastSQLite(), GetLeafNodeTaxids(), x_SanityCheck(), and ~CTaxonomy4BlastSQLite().

◆ m_DbName

string CTaxonomy4BlastSQLite::m_DbName
private

SQLite3 database file name.

Definition at line 68 of file tax4blastsqlite.hpp.

Referenced by CTaxonomy4BlastSQLite(), and x_SanityCheck().

◆ m_Statement

unique_ptr<CSQLITE_Statement> CTaxonomy4BlastSQLite::m_Statement
private

Most recent SQLite statement.

Definition at line 71 of file tax4blastsqlite.hpp.

Referenced by GetLeafNodeTaxids(), and ~CTaxonomy4BlastSQLite().


The documentation for this class was generated from the following files:
Modified on Thu Feb 29 12:24:21 2024 by modify_doxy.py rev. 669887