Search Toolkit Book for CBlastOptionsRemote
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< Uint8 > | TCounter |
| 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... | |
| CBlastOptionsRemote & | operator= (const CBlastOptionsRemote &optsRemote) |
| Assignment operator. More... | |
| TBlast4Opts * | GetBlast4AlgoOpts () |
| 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... | |
| CObject & | operator= (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:
- src/algo/blast/api/blast_options_cxx.cpp
