Search Toolkit Book for CPHIBlastNuclOptionsHandle
Handle to the nuclein PHI BLAST options. More...
#include <algo/blast/api/phiblast_nucl_options.hpp>
Inheritance diagram for CPHIBlastNuclOptionsHandle:
Collaboration diagram for CPHIBlastNuclOptionsHandle:
Public Member Functions | |
| CPHIBlastNuclOptionsHandle (EAPILocality locality=CBlastOptions::eLocal) | |
| Creates object with default options set. More... | |
| ~CPHIBlastNuclOptionsHandle () | |
| const char * | GetPHIPattern () const |
| Retrieves the pattern string option. More... | |
| void | SetPHIPattern (const char *p) |
| Sets the pattern string option. More... | |
| Public Member Functions inherited from CBlastNucleotideOptionsHandle | |
| CBlastNucleotideOptionsHandle (EAPILocality locality=CBlastOptions::eLocal) | |
| Creates object with default options set. More... | |
| CBlastNucleotideOptionsHandle (CRef< CBlastOptions > opt) | |
| Create Options Handle from Existing CBlastOptions Object. More... | |
| virtual void | SetDefaults () |
| Sets Defaults. More... | |
| ELookupTableType | GetLookupTableType () const |
| Returns LookupTableType. More... | |
| void | SetLookupTableType (ELookupTableType type) |
| Sets LookupTableType. More... | |
| int | GetWordSize () const |
| Returns WordSize. More... | |
| void | SetWordSize (int ws) |
| Sets WordSize. More... | |
| objects::ENa_strand | GetStrandOption () const |
| Returns StrandOption. More... | |
| void | SetStrandOption (objects::ENa_strand strand) |
| Sets StrandOption. More... | |
| bool | GetDustFiltering () const |
| Is dust filtering enabled? More... | |
| void | SetDustFiltering (bool val) |
| Enable dust filtering. More... | |
| int | GetDustFilteringLevel () const |
| Get level parameter for dust. More... | |
| void | SetDustFilteringLevel (int level) |
| Set level parameter for dust. More... | |
| int | GetDustFilteringWindow () const |
| Get window parameter for dust. More... | |
| void | SetDustFilteringWindow (int window) |
| Set window parameter for dust. More... | |
| int | GetDustFilteringLinker () const |
| Get linker parameter for dust. More... | |
| void | SetDustFilteringLinker (int linker) |
| Set linker parameter for dust. More... | |
| bool | GetRepeatFiltering () const |
| Is repeat filtering enabled? More... | |
| void | SetRepeatFiltering (bool val) |
| Enable repeat filtering. More... | |
| const char * | GetRepeatFilteringDB () const |
| Get the repeat filtering database. More... | |
| void | SetRepeatFilteringDB (const char *db) |
| Enable repeat filtering. More... | |
| int | GetWindowMaskerTaxId () const |
| Get the window masker taxid (or 0 if not set). More... | |
| void | SetWindowMaskerTaxId (int taxid) |
| Enable window masker and select a taxid (or 0 to disable). More... | |
| const char * | GetWindowMaskerDatabase () const |
| Get the window masker database name (or NULL if not set). More... | |
| void | SetWindowMaskerDatabase (const char *db) |
| Enable window masker and select a database (or NULL to disable). More... | |
| double | GetXDropoff () const |
| Returns XDropoff. More... | |
| void | SetXDropoff (double x) |
| Sets XDropoff. More... | |
| EBlastPrelimGapExt | GetGapExtnAlgorithm () const |
| Returns GapExtnAlgorithm. More... | |
| void | SetGapExtnAlgorithm (EBlastPrelimGapExt algo) |
| Sets GapExtnAlgorithm. More... | |
| EBlastTbackExt | GetGapTracebackAlgorithm () const |
| Returns GapTracebackAlgorithm. More... | |
| void | SetGapTracebackAlgorithm (EBlastTbackExt algo) |
| Sets GapTracebackAlgorithm. More... | |
| int | GetMatchReward () const |
| Returns MatchReward. More... | |
| void | SetMatchReward (int r) |
| Sets MatchReward. More... | |
| int | GetMismatchPenalty () const |
| Returns MismatchPenalty. More... | |
| void | SetMismatchPenalty (int p) |
| Sets MismatchPenalty. More... | |
| const char * | GetMatrixName () const |
| Returns MatrixName. More... | |
| void | SetMatrixName (const char *matrix) |
| Sets MatrixName. More... | |
| int | GetGapOpeningCost () const |
| Returns GapOpeningCost. More... | |
| void | SetGapOpeningCost (int g) |
| Sets GapOpeningCost. More... | |
| int | GetGapExtensionCost () const |
| Returns GapExtensionCost. More... | |
| void | SetGapExtensionCost (int e) |
| Sets GapExtensionCost. More... | |
| void | SetTraditionalBlastnDefaults () |
| Sets TraditionalBlastnDefaults. More... | |
| void | SetTraditionalMegablastDefaults () |
| Sets TraditionalMegablastDefaults. More... | |
| void | SetVecScreenDefaults () |
| Sets default options for VecScreen. More... | |
| Public Member Functions inherited from CBlastOptionsHandle | |
| 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... | |
| 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 |
Private Member Functions | |
| CPHIBlastNuclOptionsHandle (const CPHIBlastNuclOptionsHandle &rhs) | |
| Disallow copy constructor. More... | |
| CPHIBlastNuclOptionsHandle & | operator= (const CPHIBlastNuclOptionsHandle &rhs) |
| Disallow assignment operator. More... | |
Additional Inherited Members | |
| Public Types inherited from CBlastOptionsHandle | |
| 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... | |
| 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 CBlastNucleotideOptionsHandle | |
| virtual void | SetRemoteProgramAndService_Blast3 () |
| Set the program and service name for remote blast. More... | |
| virtual void | SetLookupTableDefaults () |
| Overrides LookupTableDefaults for nucleotide options. More... | |
| virtual void | SetMBLookupTableDefaults () |
| Overrides MBLookupTableDefaults for nucleotide options. More... | |
| virtual void | SetQueryOptionDefaults () |
| Overrides QueryOptionDefaults for nucleotide options. More... | |
| virtual void | SetInitialWordOptionsDefaults () |
| Overrides InitialWordOptionsDefaults for nucleotide options. More... | |
| virtual void | SetMBInitialWordOptionsDefaults () |
| Overrides MBInitialWordOptionsDefaults for nucleotide options. More... | |
| virtual void | SetGappedExtensionDefaults () |
| Overrides GappedExtensionDefaults for nucleotide options. More... | |
| virtual void | SetMBGappedExtensionDefaults () |
| Overrides MBGappedExtensionDefaults for nucleotide options. More... | |
| virtual void | SetScoringOptionsDefaults () |
| Overrides ScoringOptionsDefaults for nucleotide options. More... | |
| virtual void | SetMBScoringOptionsDefaults () |
| Overrides MBScoringOptionsDefaults for nucleotide options. More... | |
| virtual void | SetHitSavingOptionsDefaults () |
| Overrides HitSavingOptionsDefaults for nucleotide options. More... | |
| virtual void | SetMBHitSavingOptionsDefaults () |
| Overrides MBHitSavingOptionsDefaults for nucleotide options. More... | |
| virtual void | SetEffectiveLengthsOptionsDefaults () |
| Overrides EffectiveLengthsOptionsDefaults for nucleotide options. More... | |
| virtual void | SetSubjectSequenceOptionsDefaults () |
| Overrides SubjectSequenceOptionsDefaults for nucleotide options. More... | |
| Protected Member Functions inherited from CBlastOptionsHandle | |
| CBlastOptionsHandle (CRef< CBlastOptions > opt) | |
| Create Options Handle from Existing CBlastOptions Object. More... | |
| Protected Member Functions inherited from CObject | |
| virtual void | DeleteThis (void) |
| Virtual method "deleting" this object. More... | |
| Protected Attributes inherited from CBlastOptionsHandle | |
| 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... | |
Detailed Description
Handle to the nuclein PHI BLAST options.
Adapter class for PHI BLAST search. Exposes an interface to allow manipulation the options that are relevant to this type of search.
Definition at line 53 of file phiblast_nucl_options.hpp.
The documentation for this class was generated from the following files:
- include/algo/blast/api/phiblast_nucl_options.hpp
- src/algo/blast/api/phiblast_nucl_options.cpp
