Search Toolkit Book for CBlastOptionsHandle
Handle to the options to the BLAST algorithm. More...
#include <algo/blast/api/blast_options_handle.hpp>
Inheritance diagram for CBlastOptionsHandle:
Collaboration diagram for CBlastOptionsHandle:
Public Types | |
| typedef CBlastOptions::EAPILocality | EAPILocality |
| Convenience define. More... | |
| 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 | |
| CBlastOptionsHandle (EAPILocality locality) | |
| Default c-tor. More... | |
| bool | Validate () const |
| Validate the options contained in this object. More... | |
| const CBlastOptions & | GetOptions () const |
| Return the object which this object is a handle for. More... | |
| CBlastOptions & | SetOptions () |
| Returns a reference to the internal options class which this object is a handle for. More... | |
| virtual void | SetDefaults () |
| Resets the state of the object to all default values. More... | |
| void | DoneDefaults () |
| Returns true if this object needs default values set. More... | |
| int | GetWindowSize () const |
| Returns WindowSize. More... | |
| void | SetWindowSize (int ws) |
| Sets WindowSize. More... | |
| int | GetOffDiagonalRange () const |
| void | SetOffDiagonalRange (int r) |
| void | ClearFilterOptions () |
| Clears the filtering options. More... | |
| char * | GetFilterString () const |
| Returns FilterString. More... | |
| void | SetFilterString (const char *f, bool clear=true) |
| Sets FilterString. More... | |
| bool | GetMaskAtHash () const |
| Returns whether masking should only be done for lookup table creation. More... | |
| void | SetMaskAtHash (bool m=true) |
| Sets MaskAtHash. More... | |
| double | GetGapXDropoff () const |
| Returns GapXDropoff. More... | |
| void | SetGapXDropoff (double x) |
| Sets GapXDropoff. More... | |
| double | GetGapTrigger () const |
| Returns GapTrigger. More... | |
| void | SetGapTrigger (double g) |
| Sets GapTrigger. More... | |
| double | GetGapXDropoffFinal () const |
| Returns GapXDropoffFinal. More... | |
| void | SetGapXDropoffFinal (double x) |
| Sets GapXDropoffFinal. More... | |
| int | GetHitlistSize () const |
| Returns HitlistSize. More... | |
| void | SetHitlistSize (int s) |
| Sets HitlistSize. More... | |
| int | GetMaxNumHspPerSequence () const |
| Returns MaxNumHspPerSequence. More... | |
| void | SetMaxNumHspPerSequence (int m) |
| Sets MaxNumHspPerSequence. More... | |
| int | GetMaxHspsPerSubject () const |
| Returns MaxHspsPerSubjectQueryPair. More... | |
| void | SetMaxHspsPerSubject (int m) |
| Sets MaxHspPerSubjectQueryPair. More... | |
| double | GetEvalueThreshold () const |
| Returns EvalueThreshold. More... | |
| void | SetEvalueThreshold (double eval) |
| Sets EvalueThreshold. More... | |
| int | GetCutoffScore () const |
| Returns CutoffScore. More... | |
| void | SetCutoffScore (int s) |
| Sets CutoffScore. More... | |
| double | GetPercentIdentity () const |
| Returns PercentIdentity. More... | |
| void | SetPercentIdentity (double p) |
| Sets PercentIdentity. More... | |
| double | GetQueryCovHspPerc () const |
| Returns QueryCovHspPerc. More... | |
| void | SetQueryCovHspPerc (double p) |
| Sets QueryCovHspPerc. More... | |
| int | GetMinDiagSeparation () const |
| Returns MinDiagSeparation. More... | |
| void | SetMinDiagSeparation (int d) |
| Sets MinDiagSeparation. More... | |
| bool | GetGappedMode () const |
| Returns GappedMode. More... | |
| void | SetGappedMode (bool m=true) |
| Sets GappedMode. More... | |
| int | GetCullingLimit () const |
| Returns Culling limit. More... | |
| void | SetCullingLimit (int s) |
| Sets Culling limit. More... | |
| int | GetMaskLevel () const |
| Returns MaskLevel -RMH-. More... | |
| void | SetMaskLevel (int ml) |
| Sets MaskLevel -RMH-. More... | |
| bool | GetComplexityAdjMode () const |
| Returns Complexity Adjustment Mode -RMH-. More... | |
| void | SetComplexityAdjMode (bool m=true) |
| Sets ComplexityAdjMode -RMH-. More... | |
| double | GetLowScorePerc () const |
| Returns low score percentage for ungapped alignments. More... | |
| void | SetLowScorePerc (double p) |
| Sets low score percentage for ungapped alignments. More... | |
| Int8 | GetDbLength () const |
| Returns DbLength. More... | |
| void | SetDbLength (Int8 len) |
| Sets DbLength. More... | |
| unsigned int | GetDbSeqNum () const |
| Returns DbSeqNum. More... | |
| void | SetDbSeqNum (unsigned int num) |
| Sets DbSeqNum. More... | |
| Int8 | GetEffectiveSearchSpace () const |
| Returns EffectiveSearchSpace. More... | |
| void | SetEffectiveSearchSpace (Int8 eff) |
| Sets EffectiveSearchSpace. More... | |
| 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 |
Protected Member Functions | |
| CBlastOptionsHandle (CRef< CBlastOptions > opt) | |
| Create Options Handle from Existing CBlastOptions Object. More... | |
| virtual void | SetRemoteProgramAndService_Blast3 ()=0 |
| Set the program and service name for remote blast. More... | |
| virtual void | SetLookupTableDefaults ()=0 |
| Sets LookupTableDefaults. More... | |
| virtual void | SetQueryOptionDefaults ()=0 |
| Sets QueryOptionDefaults. More... | |
| virtual void | SetInitialWordOptionsDefaults ()=0 |
| Sets InitialWordOptionsDefaults. More... | |
| virtual void | SetGappedExtensionDefaults ()=0 |
| Sets GappedExtensionDefaults. More... | |
| virtual void | SetScoringOptionsDefaults ()=0 |
| Sets ScoringOptionsDefaults. More... | |
| virtual void | SetHitSavingOptionsDefaults ()=0 |
| Sets HitSavingOptionsDefaults. More... | |
| virtual void | SetEffectiveLengthsOptionsDefaults ()=0 |
| Sets EffectiveLengthsOptionsDefaults. More... | |
| virtual void | SetSubjectSequenceOptionsDefaults ()=0 |
| Sets SubjectSequenceOptionsDefaults. More... | |
| Protected Member Functions inherited from CObject | |
| virtual void | DeleteThis (void) |
| Virtual method "deleting" this object. More... | |
Protected Attributes | |
| CRef< CBlastOptions > | m_Opts |
| Data type this class controls access to. More... | |
| bool | m_DefaultsMode |
| Set to true when 'remote' options should ignore setters. More... | |
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... | |
Detailed Description
Handle to the options to the BLAST algorithm.
This abstract base class only defines those options that are truly "universal" BLAST options (they apply to all flavors of BLAST).
- Invariant
- Derived classes define options that are applicable only to those programs whose options they manipulate.
Definition at line 141 of file blast_options_handle.hpp.
The documentation for this class was generated from the following files:
- include/algo/blast/api/blast_options_handle.hpp
- src/algo/blast/api/blast_options_handle.cpp
