Search Toolkit Book for CBlastNucleotideOptionsHandle
Handle to the nucleotide-nucleotide options to the BLAST algorithm. More...
#include <algo/blast/api/blast_nucl_options.hpp>
Inheritance diagram for CBlastNucleotideOptionsHandle:
Collaboration diagram for CBlastNucleotideOptionsHandle:
Public Member Functions | |
| 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 |
Protected Member Functions | |
| 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... | |
Private Member Functions | |
| CBlastNucleotideOptionsHandle (const CBlastNucleotideOptionsHandle &rhs) | |
| Disallow copy constructor. More... | |
| CBlastNucleotideOptionsHandle & | operator= (const CBlastNucleotideOptionsHandle &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 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 nucleotide-nucleotide options to the BLAST algorithm.
Adapter class for nucleotide-nucleotide BLAST comparisons. Exposes an interface to allow manipulation the options that are relevant to this type of search.
NB: By default, traditional megablast defaults are used. If blastn defaults are desired, please call the appropriate member function:
void SetTraditionalBlastnDefaults(); void SetTraditionalMegablastDefaults();
Definition at line 58 of file blast_nucl_options.hpp.
The documentation for this class was generated from the following files:
- include/algo/blast/api/blast_nucl_options.hpp
- src/algo/blast/api/blast_nucl_options.cpp
