NCBI C++ ToolKit
Public Member Functions | Private Member Functions | Private Attributes | Static Private Attributes | List of all members
CLocalRPSBlast Class Reference

Search Toolkit Book for CLocalRPSBlast

#include <algo/blast/api/rpsblast_local.hpp>

+ Inheritance diagram for CLocalRPSBlast:
+ Collaboration diagram for CLocalRPSBlast:

Public Member Functions

 CLocalRPSBlast (CRef< CBlastQueryVector > query_vector, const string &db, CRef< CBlastOptionsHandle > options, unsigned int num_of_threads=kAutoThreadedSearch)
 
CRef< CSearchResultSetRun ()
 
 ~CLocalRPSBlast ()
 
- 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
 

Private Member Functions

 CLocalRPSBlast (const CLocalRPSBlast &)
 
CLocalRPSBlastoperator= (const CLocalRPSBlast &)
 
CRef< CSearchResultSetRunThreadedSearch ()
 
void x_AdjustDbSize (void)
 

Private Attributes

unsigned int m_num_of_threads
 
const string m_db_name
 
CRef< CBlastOptionsHandlem_opt_handle
 
CRef< CBlastQueryVectorm_query_vector
 
unsigned int m_num_of_dbs
 
vector< stringm_rps_databases
 

Static Private Attributes

static const int kDisableThreadedSearch = 1
 
static const int kAutoThreadedSearch = 0
 

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)
 
- 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...
 
- Protected Member Functions inherited from CObject
virtual void DeleteThis (void)
 Virtual method "deleting" this object. More...
 

Detailed Description

Definition at line 41 of file rpsblast_local.hpp.

Constructor & Destructor Documentation

◆ CLocalRPSBlast() [1/2]

CLocalRPSBlast::CLocalRPSBlast ( const CLocalRPSBlast )
private

◆ CLocalRPSBlast() [2/2]

CLocalRPSBlast::CLocalRPSBlast ( CRef< CBlastQueryVector query_vector,
const string db,
CRef< CBlastOptionsHandle options,
unsigned int  num_of_threads = kAutoThreadedSearch 
)

Definition at line 331 of file rpsblast_local.cpp.

◆ ~CLocalRPSBlast()

CLocalRPSBlast::~CLocalRPSBlast ( )
inline

Definition at line 93 of file rpsblast_local.hpp.

Member Function Documentation

◆ operator=()

CLocalRPSBlast& CLocalRPSBlast::operator= ( const CLocalRPSBlast )
private

◆ Run()

CRef< CSearchResultSet > CLocalRPSBlast::Run ( void  )

◆ RunThreadedSearch()

CRef< CSearchResultSet > CLocalRPSBlast::RunThreadedSearch ( void  )
private

Definition at line 409 of file rpsblast_local.cpp.

◆ x_AdjustDbSize()

void CLocalRPSBlast::x_AdjustDbSize ( void  )
private

Definition at line 349 of file rpsblast_local.cpp.

Member Data Documentation

◆ kAutoThreadedSearch

const int CLocalRPSBlast::kAutoThreadedSearch = 0
staticprivate

Definition at line 59 of file rpsblast_local.hpp.

◆ kDisableThreadedSearch

const int CLocalRPSBlast::kDisableThreadedSearch = 1
staticprivate

Definition at line 58 of file rpsblast_local.hpp.

◆ m_db_name

const string CLocalRPSBlast::m_db_name
private

Definition at line 53 of file rpsblast_local.hpp.

◆ m_num_of_dbs

unsigned int CLocalRPSBlast::m_num_of_dbs
private

Definition at line 56 of file rpsblast_local.hpp.

◆ m_num_of_threads

unsigned int CLocalRPSBlast::m_num_of_threads
private

Definition at line 52 of file rpsblast_local.hpp.

◆ m_opt_handle

CRef<CBlastOptionsHandle> CLocalRPSBlast::m_opt_handle
private

Definition at line 54 of file rpsblast_local.hpp.

◆ m_query_vector

CRef<CBlastQueryVector> CLocalRPSBlast::m_query_vector
private

Definition at line 55 of file rpsblast_local.hpp.

◆ m_rps_databases

vector<string> CLocalRPSBlast::m_rps_databases
private

Definition at line 57 of file rpsblast_local.hpp.


The documentation for this class was generated from the following files:
Modified on Tue May 28 05:51:41 2024 by modify_doxy.py rev. 669887