NCBI C++ ToolKit
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CBlastOptionsRemote Class Reference

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Encapsulates all blast input parameters. More...

+ Inheritance diagram for CBlastOptionsRemote:
+ Collaboration diagram for CBlastOptionsRemote:

Public Types

typedef ncbi::objects::CBlast4_parameters TBlast4Opts
 
typedef vector< CConstRef< objects::CSeq_loc > > TSeqLocVector
 
- 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...
 

Public Member Functions

 CBlastOptionsRemote (void)
 
 ~CBlastOptionsRemote ()
 
 CBlastOptionsRemote (const CBlastOptionsRemote &optsRemote)
 Copy constructor. More...
 
CBlastOptionsRemoteoperator= (const CBlastOptionsRemote &optsRemote)
 Assignment operator. More...
 
TBlast4OptsGetBlast4AlgoOpts ()
 
void SetValue (EBlastOptIdx opt, const EProgram &x)
 
void SetValue (EBlastOptIdx opt, const int &x)
 
void SetValue (EBlastOptIdx opt, const double &x)
 
void SetValue (EBlastOptIdx opt, const char *x)
 
void SetValue (EBlastOptIdx opt, const TSeqLocVector &x)
 
void SetValue (EBlastOptIdx opt, const ESeedContainerType &x)
 
void SetValue (EBlastOptIdx opt, const bool &x)
 
void SetValue (EBlastOptIdx opt, const Int8 &x)
 
void SetValue (EBlastOptIdx opt, const short &x)
 
void SetValue (EBlastOptIdx opt, const unsigned int &x)
 
void SetValue (EBlastOptIdx opt, const unsigned char &x)
 
void SetValue (EBlastOptIdx opt, const objects::ENa_strand &x)
 
void ResetValue (CBlast4Field &opt)
 Remove any objects matching this Blast4 field object. More...
 
void SetDefaultsMode (bool dmode)
 
bool GetDefaultsMode ()
 
- 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

void x_DoDeepCopy (const CBlastOptionsRemote &optsRemote)
 Perform a "deep copy" of remote Blast options. More...
 
template<class T >
void x_SetParam (CBlast4Field &name, T &value)
 
void x_SetOneParam (CBlast4Field &field, const int *x)
 
void x_SetOneParam (CBlast4Field &field, const char **x)
 
void x_SetOneParam (CBlast4Field &field, const bool *x)
 
void x_SetOneParam (CBlast4Field &field, CRef< objects::CBlast4_cutoff > *x)
 
void x_SetOneParam (CBlast4Field &field, const double *x)
 
void x_SetOneParam (CBlast4Field &field, const Int8 *x)
 
void x_SetOneParam (CBlast4Field &field, objects::EBlast4_strand_type *x)
 
void x_AttachValue (CRef< objects::CBlast4_parameter > p)
 
void x_ResetValue (CBlast4Field &f)
 Remove values for a given Blast4 field. More...
 
void x_Throwx (const string &msg) const
 

Private Attributes

CRef< objects::CBlast4_parameters > m_ReqOpts
 
bool m_DefaultsMode
 

Additional Inherited Members

- 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

Encapsulates all blast input parameters.

Definition at line 60 of file blast_options_cxx.cpp.


The documentation for this class was generated from the following file:
Modified on Fri May 24 14:53:52 2024 by modify_doxy.py rev. 669887