Search Toolkit Book for CBlastOptions
Encapsulates ALL the BLAST algorithm's options. More...
#include <algo/blast/api/blast_options.hpp>
Inheritance diagram for CBlastOptions:
Collaboration diagram for CBlastOptions:
Public Types | |
| enum | EAPILocality { eLocal , eRemote , eBoth } |
| Enumerates the possible contexts in which objects of this type can be used. More... | |
| typedef ncbi::objects::CBlast4_parameters | TBlast4Opts |
| This returns a list of parameters for remote searches. 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 | |
| CBlastOptions (EAPILocality locality=eLocal) | |
| Constructor which allows specification of local or remote version of the options (might change in the future) More... | |
| ~CBlastOptions () | |
| Destructor. More... | |
| CRef< CBlastOptions > | Clone () const |
| Explicit deep copy of the Blast options object. More... | |
| EAPILocality | GetLocality () const |
| Return the locality used when the object was created. More... | |
| bool | Validate () const |
| Validate the options. More... | |
| EProgram | GetProgram () const |
| Accessors/Mutators for individual options. More... | |
| void | SetProgram (EProgram p) |
| Sets the task this object is best suited for. More... | |
| EBlastProgramType | GetProgramType () const |
| Returns the CORE BLAST notion of program type. More... | |
| bool | IsIterativeSearch () const |
| double | GetWordThreshold () const |
| Returns WordThreshold. More... | |
| void | SetWordThreshold (double w) |
| Sets WordThreshold. More... | |
| ELookupTableType | GetLookupTableType () const |
| void | SetLookupTableType (ELookupTableType type) |
| int | GetWordSize () const |
| void | SetWordSize (int ws) |
| Uint4 | GetLookupTableStride () const |
| void | SetLookupTableStride (Uint4 val) |
| bool | GetLookupDbFilter (void) const |
| void | SetLookupDbFilter (bool val) |
| Uint1 | GetMaxDbWordCount (void) const |
| Get maximum word count for lookup table word masking by database frequency. More... | |
| void | SetMaxDbWordCount (Uint1 num) |
| Set maximum word count for lookup table word masking by database frequency. More... | |
| unsigned char | GetMBTemplateLength () const |
| Megablast only lookup table options. More... | |
| void | SetMBTemplateLength (unsigned char len) |
| unsigned char | GetMBTemplateType () const |
| void | SetMBTemplateType (unsigned char type) |
| void | ClearFilterOptions () |
| char * | GetFilterString () const |
| Return the filtering string used. More... | |
| void | SetFilterString (const char *f, bool clear=true) |
| bool | GetMaskAtHash () const |
| void | SetMaskAtHash (bool val=true) |
| bool | GetDustFiltering () const |
| void | SetDustFiltering (bool val=true) |
| int | GetDustFilteringLevel () const |
| void | SetDustFilteringLevel (int m) |
| int | GetDustFilteringWindow () const |
| void | SetDustFilteringWindow (int m) |
| int | GetDustFilteringLinker () const |
| void | SetDustFilteringLinker (int m) |
| bool | GetSegFiltering () const |
| void | SetSegFiltering (bool val=true) |
| int | GetSegFilteringWindow () const |
| void | SetSegFilteringWindow (int m) |
| double | GetSegFilteringLocut () const |
| void | SetSegFilteringLocut (double m) |
| double | GetSegFilteringHicut () const |
| void | SetSegFilteringHicut (double m) |
| bool | GetRepeatFiltering () const |
| Returns true if repeat filtering is on. More... | |
| void | SetRepeatFiltering (bool val=true) |
| Turns on repeat filtering using the default repeat database, namely kDefaultRepeatFilterDb. More... | |
| const char * | GetRepeatFilteringDB () const |
| Returns the name of the repeat filtering database to use. More... | |
| void | SetRepeatFilteringDB (const char *db) |
| Sets the repeat filtering database to use. More... | |
| int | GetWindowMaskerTaxId () const |
| Returns the tax id used for the windowmasker database to use, if set via SetWindowMaskerTaxId (otherwise, returns 0) More... | |
| void | SetWindowMaskerTaxId (int taxid) |
| Sets the tax id to select an appropriate windowmasker database Conversion algorithm from tax id to database name is specific to NCBI, will not work outside NCBI. More... | |
| const char * | GetWindowMaskerDatabase () const |
| Return the name of the windowmasker database to use. More... | |
| void | SetWindowMaskerDatabase (const char *db) |
| Sets the windowmasker database to use. More... | |
| bool | GetReadQualityFiltering () const |
| Returns true if next-generation read quality filtering is turned on. More... | |
| void | SetReadQualityFiltering (bool val=true) |
| Turn on/off next-generation read quality filtering with deafult parameters. More... | |
| double | GetReadMaxFractionAmbiguous () const |
| Get maximum fraction of ambiguous bases for next-generation read quality filtering. More... | |
| void | SetReadMaxFractionAmbiguous (double val) |
| Set maximum fraction of ambiguous bases for next-generation read quality filtering. More... | |
| int | GetReadMinDimerEntropy () const |
| Get minimum dimer entropy for next-generation read quality filtering. More... | |
| void | SetReadMinDimerEntropy (int val) |
| Set minimum dimer entropy for next-generation read quality filtering. More... | |
| objects::ENa_strand | GetStrandOption () const |
| void | SetStrandOption (objects::ENa_strand s) |
| int | GetQueryGeneticCode () const |
| void | SetQueryGeneticCode (int gc) |
| int | GetWindowSize () const |
| void | SetWindowSize (int w) |
| int | GetOffDiagonalRange () const |
| void | SetOffDiagonalRange (int r) |
| double | GetXDropoff () const |
| void | SetXDropoff (double x) |
| double | GetGapXDropoff () const |
| void | SetGapXDropoff (double x) |
| double | GetGapXDropoffFinal () const |
| void | SetGapXDropoffFinal (double x) |
| double | GetGapTrigger () const |
| void | SetGapTrigger (double g) |
| EBlastPrelimGapExt | GetGapExtnAlgorithm () const |
| void | SetGapExtnAlgorithm (EBlastPrelimGapExt a) |
| EBlastTbackExt | GetGapTracebackAlgorithm () const |
| void | SetGapTracebackAlgorithm (EBlastTbackExt a) |
| ECompoAdjustModes | GetCompositionBasedStats () const |
| void | SetCompositionBasedStats (ECompoAdjustModes mode) |
| bool | GetSmithWatermanMode () const |
| void | SetSmithWatermanMode (bool m=true) |
| int | GetUnifiedP () const |
| void | SetUnifiedP (int u=0) |
| int | GetMaxMismatches () const |
| void | SetMaxMismatches (int m) |
| int | GetMismatchWindow () const |
| void | SetMismatchWindow (int w) |
| int | GetHitlistSize () const |
| void | SetHitlistSize (int s) |
| int | GetMaxNumHspPerSequence () const |
| void | SetMaxNumHspPerSequence (int m) |
| int | GetMaxHspsPerSubject () const |
| void | SetMaxHspsPerSubject (int m) |
| int | GetCullingLimit () const |
| void | SetCullingLimit (int s) |
| bool | GetSubjectBestHit () const |
| void | SetSubjectBestHit () |
| double | GetBestHitOverhang () const |
| void | SetBestHitOverhang (double overhang) |
| double | GetBestHitScoreEdge () const |
| void | SetBestHitScoreEdge (double score_edge) |
| double | GetEvalueThreshold () const |
| void | SetEvalueThreshold (double eval) |
| int | GetCutoffScore () const |
| void | SetCutoffScore (int s) |
| vector< double > | GetCutoffScoreCoeffs () const |
| void | SetCutoffScoreCoeffs (const vector< double > &c) |
| double | GetPercentIdentity () const |
| void | SetPercentIdentity (double p) |
| int | GetMaxEditDistance () const |
| void | SetMaxEditDistance (int e) |
| double | GetQueryCovHspPerc () const |
| void | SetQueryCovHspPerc (double p) |
| int | GetMinDiagSeparation () const |
| void | SetMinDiagSeparation (int d) |
| bool | GetSumStatisticsMode () const |
| Sum statistics options. More... | |
| void | SetSumStatisticsMode (bool m=true) |
| int | GetLongestIntronLength () const |
| for linking HSPs with uneven gaps More... | |
| void | SetLongestIntronLength (int l) |
| for linking HSPs with uneven gaps More... | |
| bool | GetGappedMode () const |
| Returns true if gapped BLAST is set, false otherwise. More... | |
| void | SetGappedMode (bool m=true) |
| int | GetMaskLevel () const |
| Masklevel filtering option -RMH-. More... | |
| void | SetMaskLevel (int s) |
| bool | GetComplexityAdjMode () const |
| Returns true if cross_match-like complexity adjusted. More... | |
| void | SetComplexityAdjMode (bool m=true) |
| double | GetLowScorePerc () const |
| Sets a low score to drop ungapped alignments if hit list is full. More... | |
| void | SetLowScorePerc (double p=0.0) |
| bool | GetPaired () const |
| void | SetPaired (bool p) |
| bool | GetSpliceAlignments () const |
| Splice HSPs for each query (for mappring RNA-Seq reads to a genome) More... | |
| void | SetSpliceAlignments (bool s) |
| const char * | GetMatrixName () const |
| void | SetMatrixName (const char *matrix) |
| int | GetMatchReward () const |
| void | SetMatchReward (int r) |
| int | GetMismatchPenalty () const |
| void | SetMismatchPenalty (int p) |
| int | GetGapOpeningCost () const |
| void | SetGapOpeningCost (int g) |
| int | GetGapExtensionCost () const |
| void | SetGapExtensionCost (int e) |
| int | GetFrameShiftPenalty () const |
| void | SetFrameShiftPenalty (int p) |
| bool | GetOutOfFrameMode () const |
| void | SetOutOfFrameMode (bool m=true) |
| Int8 | GetDbLength () const |
| void | SetDbLength (Int8 l) |
| unsigned int | GetDbSeqNum () const |
| void | SetDbSeqNum (unsigned int n) |
| Int8 | GetEffectiveSearchSpace () const |
| void | SetEffectiveSearchSpace (Int8 eff) |
| void | SetEffectiveSearchSpace (const vector< Int8 > &eff) |
| int | GetDbGeneticCode () const |
| void | SetDbGeneticCode (int gc) |
| const char * | GetPHIPattern () const |
| void | SetPHIPattern (const char *pattern, bool is_dna) |
| double | GetInclusionThreshold () const |
| void | SetInclusionThreshold (double u) |
| int | GetPseudoCount () const |
| void | SetPseudoCount (int u) |
| bool | GetIgnoreMsaMaster () const |
| void | SetIgnoreMsaMaster (bool val) |
| double | GetDomainInclusionThreshold (void) const |
| void | SetDomainInclusionThreshold (double th) |
| bool | GetUseIndex () const |
| bool | GetForceIndex () const |
| bool | GetIsOldStyleMBIndex () const |
| bool | GetMBIndexLoaded () const |
| const string | GetIndexName () const |
| void | SetMBIndexLoaded (bool index_loaded=true) |
| void | SetUseIndex (bool use_index=true, const string &index_name="", bool force_index=false, bool old_style_index=false) |
| void | DebugDump (CDebugDumpContext ddc, unsigned int depth) const |
| Allows to dump a snapshot of the object. More... | |
| void | DoneDefaults () const |
| TBlast4Opts * | GetBlast4AlgoOpts () |
| bool | operator== (const CBlastOptions &rhs) const |
| bool | operator!= (const CBlastOptions &rhs) const |
| void | SetRemoteProgramAndService_Blast3 (const string &p, const string &s) |
| Set the program and service name for remote blast. More... | |
| virtual void | GetRemoteProgramAndService_Blast3 (string &p, string &s) const |
| Get the program and service name for remote blast. More... | |
| const CBlastOptionsMemento * | CreateSnapshot () const |
| Create a snapshot of the state of this object for internal use of its data structures (BLAST C++ APIs only) More... | |
| void | SetDefaultsMode (bool dmode) |
| If this is true, remote options will ignore "Set" calls. More... | |
| bool | GetDefaultsMode () const |
| 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... | |
| 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 Attributes | |
| CBlastOptionsLocal * | m_Local |
| CBlastOptionsRemote * | m_Remote |
| string | m_ProgramName |
| Program Name for Blast3. More... | |
| string | m_ServiceName |
| Service Name for Blast3. More... | |
| bool | m_DefaultsMode |
| Defaults mode (remote options will ignore Set ops). More... | |
| CAutomaticGenCodeSingleton | m_GenCodeSingletonVar |
| This field is add. More... | |
Friends | |
| class | CBl2Seq |
| class | CDbBlast |
| class | CDbBlastTraceback |
| class | CDbBlastPrelim |
| class | CEffectiveSearchSpacesMemento |
| class | ::CBlastTabularFormatThread |
| class | ::CTracebackTestFixture |
| class | ::CBlastSetupTestFixture |
| class | ::CUniformSearchTest |
| class | ::CTracebackSearchTestFixture |
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 the BLAST algorithm's options.
To ensure that the default options are set properly, it is recommended that this object is not created directly by the calling code, instead, it should be obtained from calling CBlastOptionsHandle::[GS]etOptions().
- Note
- This class provides accessors and mutators for all BLAST options without preventing the caller from setting inconsistent options.
- See also
- C++ BLAST Options Cookbook
Definition at line 84 of file blast_options.hpp.
Member Typedef Documentation
◆ TBlast4Opts
| typedef ncbi::objects::CBlast4_parameters CBlastOptions::TBlast4Opts |
This returns a list of parameters for remote searches.
Definition at line 479 of file blast_options.hpp.
Member Enumeration Documentation
◆ EAPILocality
Enumerates the possible contexts in which objects of this type can be used.
| Enumerator | |
|---|---|
| eLocal | To be used for running BLAST locally.
|
| eRemote | To be used when running BLAST remotely.
|
| eBoth | |
Definition at line 89 of file blast_options.hpp.
Constructor & Destructor Documentation
◆ CBlastOptions()
|
private |
Prohibit copy c-tor.
Member Function Documentation
◆ GetRemoteProgramAndService_Blast3()
|
inlinevirtual |
Get the program and service name for remote blast.
Definition at line 495 of file blast_options.hpp.
References _ASSERT, m_ProgramName, m_Remote, and m_ServiceName.
Referenced by BOOST_AUTO_TEST_CASE(), CRemoteBlast::x_Init(), and CExportStrategy::x_Process_BlastOptions().
◆ operator=()
|
private |
Prohibit assignment operator.
◆ SetRemoteProgramAndService_Blast3()
Set the program and service name for remote blast.
Definition at line 488 of file blast_options.hpp.
References m_ProgramName, and m_ServiceName.
Referenced by CBlastNucleotideOptionsHandle::SetTraditionalBlastnDefaults(), CBlastNucleotideOptionsHandle::SetTraditionalMegablastDefaults(), and CBlastNucleotideOptionsHandle::SetVecScreenDefaults().
Friends And Related Function Documentation
◆ ::CBlastSetupTestFixture
|
friend |
Definition at line 573 of file blast_options.hpp.
◆ ::CBlastTabularFormatThread
|
friend |
Definition at line 569 of file blast_options.hpp.
◆ ::CTracebackSearchTestFixture
|
friend |
Definition at line 575 of file blast_options.hpp.
◆ ::CTracebackTestFixture
|
friend |
Definition at line 572 of file blast_options.hpp.
◆ ::CUniformSearchTest
|
friend |
Definition at line 574 of file blast_options.hpp.
◆ CBl2Seq
|
friend |
Definition at line 561 of file blast_options.hpp.
◆ CDbBlast
|
friend |
Definition at line 562 of file blast_options.hpp.
◆ CDbBlastPrelim
|
friend |
Definition at line 564 of file blast_options.hpp.
◆ CDbBlastTraceback
|
friend |
Definition at line 563 of file blast_options.hpp.
◆ CEffectiveSearchSpacesMemento
|
friend |
Definition at line 565 of file blast_options.hpp.
Member Data Documentation
◆ m_DefaultsMode
|
private |
Defaults mode (remote options will ignore Set ops).
Definition at line 528 of file blast_options.hpp.
Referenced by x_DoDeepCopy().
◆ m_GenCodeSingletonVar
|
private |
This field is add.
Definition at line 559 of file blast_options.hpp.
Referenced by SetDbGeneticCode(), and SetQueryGeneticCode().
◆ m_Local
|
private |
Definition at line 518 of file blast_options.hpp.
Referenced by CBlastOptions(), CEffectiveSearchSpacesMemento::CEffectiveSearchSpacesMemento(), CreateSnapshot(), DebugDump(), GetBestHitOverhang(), GetBestHitScoreEdge(), GetComplexityAdjMode(), GetCompositionBasedStats(), GetCullingLimit(), GetCutoffScore(), GetCutoffScoreCoeffs(), GetDbGeneticCode(), GetDbLength(), GetDbOpts(), GetDbSeqNum(), GetDomainInclusionThreshold(), GetDustFiltering(), GetDustFilteringLevel(), GetDustFilteringLinker(), GetDustFilteringWindow(), GetEffectiveSearchSpace(), GetEffLenOpts(), GetEvalueThreshold(), GetExtnOpts(), GetFilterString(), GetForceIndex(), GetFrameShiftPenalty(), GetGapExtensionCost(), GetGapExtnAlgorithm(), GetGapOpeningCost(), GetGappedMode(), GetGapTracebackAlgorithm(), GetGapTrigger(), GetGapXDropoff(), GetGapXDropoffFinal(), GetHitlistSize(), GetHitSaveOpts(), GetIgnoreMsaMaster(), GetInclusionThreshold(), GetIndexName(), GetInitWordOpts(), GetIsOldStyleMBIndex(), GetLocality(), GetLongestIntronLength(), GetLookupDbFilter(), GetLookupTableStride(), GetLookupTableType(), GetLowScorePerc(), GetLutOpts(), GetMaskAtHash(), GetMaskLevel(), GetMatchReward(), GetMatrixName(), GetMaxDbWordCount(), GetMaxEditDistance(), GetMaxHspsPerSubject(), GetMaxMismatches(), GetMaxNumHspPerSequence(), GetMBIndexLoaded(), GetMBTemplateLength(), GetMBTemplateType(), GetMinDiagSeparation(), GetMismatchPenalty(), GetMismatchWindow(), GetOffDiagonalRange(), GetOutOfFrameMode(), GetPaired(), GetPercentIdentity(), GetPHIPattern(), GetProgram(), GetProgramType(), GetPseudoCount(), GetPSIBlastOpts(), GetQueryCovHspPerc(), GetQueryGeneticCode(), GetQueryOpts(), GetReadMaxFractionAmbiguous(), GetReadMinDimerEntropy(), GetReadQualityFiltering(), GetRepeatFiltering(), GetRepeatFilteringDB(), GetScoringOpts(), GetSegFiltering(), GetSegFilteringHicut(), GetSegFilteringLocut(), GetSegFilteringWindow(), GetSmithWatermanMode(), GetSpliceAlignments(), GetStrandOption(), GetSubjectBestHit(), GetSumStatisticsMode(), GetUnifiedP(), GetUseIndex(), GetWindowMaskerDatabase(), GetWindowMaskerTaxId(), GetWindowSize(), GetWordSize(), GetWordThreshold(), GetXDropoff(), operator==(), SetBestHitOverhang(), SetBestHitScoreEdge(), SetComplexityAdjMode(), SetCompositionBasedStats(), SetCullingLimit(), SetCutoffScore(), SetCutoffScoreCoeffs(), SetDbGeneticCode(), SetDbLength(), SetDbSeqNum(), SetDomainInclusionThreshold(), SetDustFiltering(), SetDustFilteringLevel(), SetDustFilteringLinker(), SetDustFilteringWindow(), SetEffectiveSearchSpace(), SetEvalueThreshold(), SetFilterString(), SetFrameShiftPenalty(), SetGapExtensionCost(), SetGapExtnAlgorithm(), SetGapOpeningCost(), SetGappedMode(), SetGapTracebackAlgorithm(), SetGapTrigger(), SetGapXDropoff(), SetGapXDropoffFinal(), SetHitlistSize(), SetIgnoreMsaMaster(), SetInclusionThreshold(), SetLongestIntronLength(), SetLookupDbFilter(), SetLookupTableStride(), SetLookupTableType(), SetLowScorePerc(), SetMaskAtHash(), SetMaskLevel(), SetMatchReward(), SetMatrixName(), SetMaxDbWordCount(), SetMaxEditDistance(), SetMaxHspsPerSubject(), SetMaxMismatches(), SetMaxNumHspPerSequence(), SetMBIndexLoaded(), SetMBTemplateLength(), SetMBTemplateType(), SetMinDiagSeparation(), SetMismatchPenalty(), SetMismatchWindow(), SetOffDiagonalRange(), SetOutOfFrameMode(), SetPaired(), SetPercentIdentity(), SetPHIPattern(), SetProgram(), SetPseudoCount(), SetQueryCovHspPerc(), SetQueryGeneticCode(), SetReadMaxFractionAmbiguous(), SetReadMinDimerEntropy(), SetReadQualityFiltering(), SetRepeatFiltering(), SetRepeatFilteringDB(), SetSegFiltering(), SetSegFilteringHicut(), SetSegFilteringLocut(), SetSegFilteringWindow(), SetSmithWatermanMode(), SetSpliceAlignments(), SetStrandOption(), SetSubjectBestHit(), SetSumStatisticsMode(), SetUnifiedP(), SetUseIndex(), SetWindowMaskerDatabase(), SetWindowMaskerTaxId(), SetWindowSize(), SetWordSize(), SetWordThreshold(), SetXDropoff(), Validate(), x_DoDeepCopy(), ~CBlastOptions(), and CEffectiveSearchSpacesMemento::~CEffectiveSearchSpacesMemento().
◆ m_ProgramName
|
private |
Program Name for Blast3.
Definition at line 522 of file blast_options.hpp.
Referenced by GetRemoteProgramAndService_Blast3(), SetRemoteProgramAndService_Blast3(), and x_DoDeepCopy().
◆ m_Remote
|
private |
Definition at line 519 of file blast_options.hpp.
Referenced by CBlastOptions(), DoneDefaults(), GetBlast4AlgoOpts(), GetDefaultsMode(), GetLocality(), GetRemoteProgramAndService_Blast3(), SetBestHitOverhang(), SetBestHitScoreEdge(), SetComplexityAdjMode(), SetCompositionBasedStats(), SetCullingLimit(), SetCutoffScore(), SetDbGeneticCode(), SetDbLength(), SetDbSeqNum(), SetDefaultsMode(), SetDomainInclusionThreshold(), SetDustFiltering(), SetDustFilteringLevel(), SetDustFilteringLinker(), SetDustFilteringWindow(), SetEffectiveSearchSpace(), SetEvalueThreshold(), SetFilterString(), SetFrameShiftPenalty(), SetGapExtensionCost(), SetGapExtnAlgorithm(), SetGapOpeningCost(), SetGappedMode(), SetGapTracebackAlgorithm(), SetGapTrigger(), SetGapXDropoff(), SetGapXDropoffFinal(), SetHitlistSize(), SetIgnoreMsaMaster(), SetInclusionThreshold(), SetLongestIntronLength(), SetLookupTableType(), SetMaskAtHash(), SetMaskLevel(), SetMatchReward(), SetMatrixName(), SetMaxEditDistance(), SetMaxHspsPerSubject(), SetMaxNumHspPerSequence(), SetMBTemplateLength(), SetMBTemplateType(), SetMismatchPenalty(), SetOutOfFrameMode(), SetPercentIdentity(), SetPHIPattern(), SetProgram(), SetPseudoCount(), SetQueryCovHspPerc(), SetQueryGeneticCode(), SetRepeatFiltering(), SetRepeatFilteringDB(), SetSegFiltering(), SetSegFilteringHicut(), SetSegFilteringLocut(), SetSegFilteringWindow(), SetSmithWatermanMode(), SetStrandOption(), SetSubjectBestHit(), SetSumStatisticsMode(), SetUnifiedP(), SetUseIndex(), SetWindowMaskerDatabase(), SetWindowMaskerTaxId(), SetWindowSize(), SetWordSize(), SetWordThreshold(), SetXDropoff(), x_DoDeepCopy(), and ~CBlastOptions().
◆ m_ServiceName
|
private |
Service Name for Blast3.
Definition at line 525 of file blast_options.hpp.
Referenced by GetRemoteProgramAndService_Blast3(), SetRemoteProgramAndService_Blast3(), and x_DoDeepCopy().
The documentation for this class was generated from the following files:
- include/algo/blast/api/blast_options.hpp
- src/algo/blast/api/blast_options_cxx.cpp
