NCBI C++ ToolKit
CBlastOptions Member List

This is the complete list of members for CBlastOptions, including all inherited members.

::CBlastSetupTestFixture classCBlastOptionsfriend
::CBlastTabularFormatThread classCBlastOptionsfriend
::CTracebackSearchTestFixture classCBlastOptionsfriend
::CTracebackTestFixture classCBlastOptionsfriend
::CUniformSearchTest classCBlastOptionsfriend
AddReference(void) constCObjectinline
CanBeDeleted(void) const THROWS_NONECObjectinline
CBl2Seq classCBlastOptionsfriend
CBlastOptions(EAPILocality locality=eLocal)CBlastOptions
CBlastOptions(const CBlastOptions &bo)CBlastOptionsprivate
CDbBlast classCBlastOptionsfriend
CDbBlastPrelim classCBlastOptionsfriend
CDbBlastTraceback classCBlastOptionsfriend
CDebugDumpable(void)CDebugDumpableinline
CEffectiveSearchSpacesMemento classCBlastOptionsfriend
CheckReferenceOverflow(TCount count) constCObjectprivate
ClearFilterOptions()CBlastOptions
Clone() constCBlastOptions
CObject(void)CObject
CObject(const CObject &src)CObject
CreateSnapshot() constCBlastOptions
DebugDump(CDebugDumpContext ddc, unsigned int depth) constCBlastOptionsvirtual
DebugDumpFormat(CDebugDumpFormatter &ddf, const string &bundle, unsigned int depth) constCDebugDumpable
DebugDumpText(ostream &out, const string &bundle, unsigned int depth) constCDebugDumpable
DeleteThis(void)CObjectprotectedvirtual
DoDeleteThisObject(void)CObjectvirtual
DoneDefaults() constCBlastOptions
DoNotDeleteThisObject(void)CObjectvirtual
DumpToConsole(void) constCDebugDumpable
EAllocFillMode enum nameCObject
eAllocFillNone enum valueCObject
eAllocFillPattern enum valueCObject
eAllocFillZero enum valueCObject
EAPILocality enum nameCBlastOptions
eBoth enum valueCBlastOptions
eCounterBitsCanBeDeletedCObjectstatic
eCounterBitsInPlainHeapCObjectstatic
eCounterBitsPlaceMaskCObjectstatic
eCounterStateMaskCObjectstatic
eCounterStepCObjectstatic
eCounterValidCObjectstatic
eLocal enum valueCBlastOptions
EnableDebugDump(bool on)CDebugDumpablestatic
eRemote enum valueCBlastOptions
GetAllocFillMode(void)CObjectstatic
GetBestHitOverhang() constCBlastOptions
GetBestHitScoreEdge() constCBlastOptions
GetBlast4AlgoOpts()CBlastOptions
GetComplexityAdjMode() constCBlastOptions
GetCompositionBasedStats() constCBlastOptions
GetCullingLimit() constCBlastOptions
GetCutoffScore() constCBlastOptions
GetCutoffScoreCoeffs() constCBlastOptions
GetDbGeneticCode() constCBlastOptions
GetDbLength() constCBlastOptions
GetDbOpts() constCBlastOptionsprivate
GetDbSeqNum() constCBlastOptions
GetDefaultsMode() constCBlastOptions
GetDomainInclusionThreshold(void) constCBlastOptions
GetDustFiltering() constCBlastOptions
GetDustFilteringLevel() constCBlastOptions
GetDustFilteringLinker() constCBlastOptions
GetDustFilteringWindow() constCBlastOptions
GetEffectiveSearchSpace() constCBlastOptions
GetEffLenOpts() constCBlastOptionsprivate
GetEvalueThreshold() constCBlastOptions
GetExtnOpts() constCBlastOptionsprivate
GetFilterString() constCBlastOptions
GetForceIndex() constCBlastOptions
GetFrameShiftPenalty() constCBlastOptions
GetGapExtensionCost() constCBlastOptions
GetGapExtnAlgorithm() constCBlastOptions
GetGapOpeningCost() constCBlastOptions
GetGappedMode() constCBlastOptions
GetGapTracebackAlgorithm() constCBlastOptions
GetGapTrigger() constCBlastOptions
GetGapXDropoff() constCBlastOptions
GetGapXDropoffFinal() constCBlastOptions
GetHitlistSize() constCBlastOptions
GetHitSaveOpts() constCBlastOptionsprivate
GetIgnoreMsaMaster() constCBlastOptions
GetInclusionThreshold() constCBlastOptions
GetIndexName() constCBlastOptions
GetInitWordOpts() constCBlastOptionsprivate
GetIsOldStyleMBIndex() constCBlastOptions
GetLocality() constCBlastOptions
GetLongestIntronLength() constCBlastOptions
GetLookupDbFilter(void) constCBlastOptions
GetLookupTableStride() constCBlastOptions
GetLookupTableType() constCBlastOptions
GetLowScorePerc() constCBlastOptions
GetLutOpts() constCBlastOptionsprivate
GetMaskAtHash() constCBlastOptions
GetMaskLevel() constCBlastOptions
GetMatchReward() constCBlastOptions
GetMatrixName() constCBlastOptions
GetMaxDbWordCount(void) constCBlastOptions
GetMaxEditDistance() constCBlastOptions
GetMaxHspsPerSubject() constCBlastOptions
GetMaxMismatches() constCBlastOptions
GetMaxNumHspPerSequence() constCBlastOptions
GetMBIndexLoaded() constCBlastOptions
GetMBTemplateLength() constCBlastOptions
GetMBTemplateType() constCBlastOptions
GetMinDiagSeparation() constCBlastOptions
GetMismatchPenalty() constCBlastOptions
GetMismatchWindow() constCBlastOptions
GetOffDiagonalRange() constCBlastOptions
GetOutOfFrameMode() constCBlastOptions
GetPaired() constCBlastOptions
GetPercentIdentity() constCBlastOptions
GetPHIPattern() constCBlastOptions
GetProgram() constCBlastOptions
GetProgramType() constCBlastOptions
GetPseudoCount() constCBlastOptions
GetPSIBlastOpts() constCBlastOptionsprivate
GetQueryCovHspPerc() constCBlastOptions
GetQueryGeneticCode() constCBlastOptions
GetQueryOpts() constCBlastOptionsprivate
GetReadMaxFractionAmbiguous() constCBlastOptions
GetReadMinDimerEntropy() constCBlastOptions
GetReadQualityFiltering() constCBlastOptions
GetRemoteProgramAndService_Blast3(string &p, string &s) constCBlastOptionsinlinevirtual
GetRepeatFiltering() constCBlastOptions
GetRepeatFilteringDB() constCBlastOptions
GetScoringOpts() constCBlastOptionsprivate
GetSegFiltering() constCBlastOptions
GetSegFilteringHicut() constCBlastOptions
GetSegFilteringLocut() constCBlastOptions
GetSegFilteringWindow() constCBlastOptions
GetSmithWatermanMode() constCBlastOptions
GetSpliceAlignments() constCBlastOptions
GetStrandOption() constCBlastOptions
GetSubjectBestHit() constCBlastOptions
GetSumStatisticsMode() constCBlastOptions
GetUnifiedP() constCBlastOptions
GetUseIndex() constCBlastOptions
GetWindowMaskerDatabase() constCBlastOptions
GetWindowMaskerTaxId() constCBlastOptions
GetWindowSize() constCBlastOptions
GetWordSize() constCBlastOptions
GetWordThreshold() constCBlastOptions
GetXDropoff() constCBlastOptions
InitCounter(void)CObjectinlineprivate
InvalidObject(void) constCObjectprivate
IsAllocatedInPool(void) const THROWS_NONECObjectinline
IsIterativeSearch() constCBlastOptions
m_CounterCObjectmutableprivate
m_DefaultsModeCBlastOptionsprivate
m_GenCodeSingletonVarCBlastOptionsprivate
m_LocalCBlastOptionsprivate
m_ProgramNameCBlastOptionsprivate
m_RemoteCBlastOptionsprivate
m_ServiceNameCBlastOptionsprivate
ObjectStateCanBeDeleted(TCount count)CObjectinlineprivatestatic
ObjectStateIsAllocatedInPool(TCount count)CObjectinlineprivatestatic
ObjectStateReferenced(TCount count)CObjectinlineprivatestatic
ObjectStateReferencedOnlyOnce(TCount count)CObjectinlineprivatestatic
ObjectStateUnreferenced(TCount count)CObjectinlineprivatestatic
ObjectStateValid(TCount count)CObjectinlineprivatestatic
operator delete(void *ptr)CObject
operator delete(void *ptr, void *place)CObject
operator delete(void *ptr, CObjectMemoryPool *place)CObject
operator delete[](void *ptr)CObject
operator new(size_t size)CObject
operator new(size_t size, void *place)CObject
operator new(size_t size, CObjectMemoryPool *place)CObject
operator new[](size_t size)CObject
operator!=(const CBlastOptions &rhs) constCBlastOptions
operator=(const CBlastOptions &bo)CBlastOptionsprivate
CObject::operator=(const CObject &src) THROWS_NONECObjectinline
operator==(const CBlastOptions &rhs) constCBlastOptions
Referenced(void) const THROWS_NONECObjectinline
ReferencedOnlyOnce(void) const THROWS_NONECObjectinline
ReleaseReference(void) constCObject
RemoveLastReference(TCount count) constCObjectprivate
RemoveReference(void) constCObjectinline
SetAllocFillMode(EAllocFillMode mode)CObjectstatic
SetAllocFillMode(const string &value)CObjectstatic
SetBestHitOverhang(double overhang)CBlastOptions
SetBestHitScoreEdge(double score_edge)CBlastOptions
SetComplexityAdjMode(bool m=true)CBlastOptions
SetCompositionBasedStats(ECompoAdjustModes mode)CBlastOptions
SetCullingLimit(int s)CBlastOptions
SetCutoffScore(int s)CBlastOptions
SetCutoffScoreCoeffs(const vector< double > &c)CBlastOptions
SetDbGeneticCode(int gc)CBlastOptions
SetDbLength(Int8 l)CBlastOptions
SetDbSeqNum(unsigned int n)CBlastOptions
SetDefaultsMode(bool dmode)CBlastOptions
SetDomainInclusionThreshold(double th)CBlastOptions
SetDustFiltering(bool val=true)CBlastOptions
SetDustFilteringLevel(int m)CBlastOptions
SetDustFilteringLinker(int m)CBlastOptions
SetDustFilteringWindow(int m)CBlastOptions
SetEffectiveSearchSpace(Int8 eff)CBlastOptions
SetEffectiveSearchSpace(const vector< Int8 > &eff)CBlastOptions
SetEvalueThreshold(double eval)CBlastOptions
SetFilterString(const char *f, bool clear=true)CBlastOptions
SetFrameShiftPenalty(int p)CBlastOptions
SetGapExtensionCost(int e)CBlastOptions
SetGapExtnAlgorithm(EBlastPrelimGapExt a)CBlastOptions
SetGapOpeningCost(int g)CBlastOptions
SetGappedMode(bool m=true)CBlastOptions
SetGapTracebackAlgorithm(EBlastTbackExt a)CBlastOptions
SetGapTrigger(double g)CBlastOptions
SetGapXDropoff(double x)CBlastOptions
SetGapXDropoffFinal(double x)CBlastOptions
SetHitlistSize(int s)CBlastOptions
SetIgnoreMsaMaster(bool val)CBlastOptions
SetInclusionThreshold(double u)CBlastOptions
SetLongestIntronLength(int l)CBlastOptions
SetLookupDbFilter(bool val)CBlastOptions
SetLookupTableStride(Uint4 val)CBlastOptions
SetLookupTableType(ELookupTableType type)CBlastOptions
SetLowScorePerc(double p=0.0)CBlastOptions
SetMaskAtHash(bool val=true)CBlastOptions
SetMaskLevel(int s)CBlastOptions
SetMatchReward(int r)CBlastOptions
SetMatrixName(const char *matrix)CBlastOptions
SetMaxDbWordCount(Uint1 num)CBlastOptions
SetMaxEditDistance(int e)CBlastOptions
SetMaxHspsPerSubject(int m)CBlastOptions
SetMaxMismatches(int m)CBlastOptions
SetMaxNumHspPerSequence(int m)CBlastOptions
SetMBIndexLoaded(bool index_loaded=true)CBlastOptions
SetMBTemplateLength(unsigned char len)CBlastOptions
SetMBTemplateType(unsigned char type)CBlastOptions
SetMinDiagSeparation(int d)CBlastOptions
SetMismatchPenalty(int p)CBlastOptions
SetMismatchWindow(int w)CBlastOptions
SetOffDiagonalRange(int r)CBlastOptions
SetOutOfFrameMode(bool m=true)CBlastOptions
SetPaired(bool p)CBlastOptions
SetPercentIdentity(double p)CBlastOptions
SetPHIPattern(const char *pattern, bool is_dna)CBlastOptions
SetProgram(EProgram p)CBlastOptions
SetPseudoCount(int u)CBlastOptions
SetQueryCovHspPerc(double p)CBlastOptions
SetQueryGeneticCode(int gc)CBlastOptions
SetReadMaxFractionAmbiguous(double val)CBlastOptions
SetReadMinDimerEntropy(int val)CBlastOptions
SetReadQualityFiltering(bool val=true)CBlastOptions
SetRemoteProgramAndService_Blast3(const string &p, const string &s)CBlastOptionsinline
SetRepeatFiltering(bool val=true)CBlastOptions
SetRepeatFilteringDB(const char *db)CBlastOptions
SetSegFiltering(bool val=true)CBlastOptions
SetSegFilteringHicut(double m)CBlastOptions
SetSegFilteringLocut(double m)CBlastOptions
SetSegFilteringWindow(int m)CBlastOptions
SetSmithWatermanMode(bool m=true)CBlastOptions
SetSpliceAlignments(bool s)CBlastOptions
SetStrandOption(objects::ENa_strand s)CBlastOptions
SetSubjectBestHit()CBlastOptions
SetSumStatisticsMode(bool m=true)CBlastOptions
SetUnifiedP(int u=0)CBlastOptions
SetUseIndex(bool use_index=true, const string &index_name="", bool force_index=false, bool old_style_index=false)CBlastOptions
SetWindowMaskerDatabase(const char *db)CBlastOptions
SetWindowMaskerTaxId(int taxid)CBlastOptions
SetWindowSize(int w)CBlastOptions
SetWordSize(int ws)CBlastOptions
SetWordThreshold(double w)CBlastOptions
SetXDropoff(double x)CBlastOptions
sm_DumpEnabledCDebugDumpableprivatestatic
TBlast4Opts typedefCBlastOptions
TCount typedefCObject
TCounter typedefCObject
ThrowNullPointerException(void)CObjectstatic
ThrowNullPointerException(const type_info &type)CObjectstatic
TLockerType typedefCObject
Validate() constCBlastOptions
x_DoDeepCopy(const CBlastOptions &opts)CBlastOptionsprivate
x_Throwx(const string &msg) constCBlastOptionsprivate
~CBlastOptions()CBlastOptions
~CDebugDumpable(void)CDebugDumpablevirtual
~CObject(void)CObjectvirtual
Modified on Fri Mar 01 10:08:35 2024 by modify_doxy.py rev. 669887