CBlastOptionsHandle Class Reference
[BLAST (Basic Local Alignment Search Tool)]

Search Toolkit Book for CBlastOptionsHandle

#include <blast_options_handle.hpp>

Inheritance diagram for CBlastOptionsHandle:

[legend]Collaboration diagram for CBlastOptionsHandle:

[legend]List of all members.

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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).

See also:

C++ BLAST Options Cookbook C++ BLAST Options Design

Invariant:

Derived classes define options that are applicable only to those programs whose options they manipulate.

Definition at line 140 of file blast_options_handle.hpp.

Public Types
typedef CBlastOptions::EAPILocality	EAPILocality
	Convenience define.
Public Member Functions
	CBlastOptionsHandle (EAPILocality locality)
	Default c-tor.
bool	Validate () const
	Validate the options contained in this object.
const CBlastOptions &	GetOptions () const
	Return the object which this object is a handle for.
CBlastOptions &	SetOptions ()
	Returns a reference to the internal options class which this object is a handle for.
virtual void	SetDefaults ()
	Resets the state of the object to all default values.
void	DoneDefaults ()
	Returns true if this object needs default values set.
int	GetWindowSize () const
	Returns WindowSize.
void	SetWindowSize (int ws)
	Sets WindowSize.
int	GetOffDiagonalRange () const
void	SetOffDiagonalRange (int r)
void	ClearFilterOptions ()
	Clears the filtering options.
char *	GetFilterString () const
	Returns FilterString.
void	SetFilterString (const char *f, bool clear=true)
	Sets FilterString.
bool	GetMaskAtHash () const
	Returns whether masking should only be done for lookup table creation.
void	SetMaskAtHash (bool m=true)
	Sets MaskAtHash.
double	GetGapXDropoff () const
	Returns GapXDropoff.
void	SetGapXDropoff (double x)
	Sets GapXDropoff.
double	GetGapTrigger () const
	Returns GapTrigger.
void	SetGapTrigger (double g)
	Sets GapTrigger.
double	GetGapXDropoffFinal () const
	Returns GapXDropoffFinal.
void	SetGapXDropoffFinal (double x)
	Sets GapXDropoffFinal.
int	GetHitlistSize () const
	Returns HitlistSize.
void	SetHitlistSize (int s)
	Sets HitlistSize.
int	GetMaxNumHspPerSequence () const
	Returns MaxNumHspPerSequence.
void	SetMaxNumHspPerSequence (int m)
	Sets MaxNumHspPerSequence.
double	GetEvalueThreshold () const
	Returns EvalueThreshold.
void	SetEvalueThreshold (double eval)
	Sets EvalueThreshold.
int	GetCutoffScore () const
	Returns CutoffScore.
void	SetCutoffScore (int s)
	Sets CutoffScore.
double	GetPercentIdentity () const
	Returns PercentIdentity.
void	SetPercentIdentity (double p)
	Sets PercentIdentity.
int	GetMinDiagSeparation () const
	Returns MinDiagSeparation.
void	SetMinDiagSeparation (int d)
	Sets MinDiagSeparation.
bool	GetGappedMode () const
	Returns GappedMode.
void	SetGappedMode (bool m=true)
	Sets GappedMode.
int	GetCullingLimit () const
	Returns Culling limit.
void	SetCullingLimit (int s)
	Sets Culling limit.
Int8	GetDbLength () const
	Returns DbLength.
void	SetDbLength (Int8 len)
	Sets DbLength.
unsigned int	GetDbSeqNum () const
	Returns DbSeqNum.
void	SetDbSeqNum (unsigned int num)
	Sets DbSeqNum.
Int8	GetEffectiveSearchSpace () const
	Returns EffectiveSearchSpace.
void	SetEffectiveSearchSpace (Int8 eff)
	Sets EffectiveSearchSpace.
Protected Member Functions
virtual void	SetRemoteProgramAndService_Blast3 ()=0
	Set the program and service name for remote blast.
virtual void	SetLookupTableDefaults ()=0
	Sets LookupTableDefaults.
virtual void	SetQueryOptionDefaults ()=0
	Sets QueryOptionDefaults.
virtual void	SetInitialWordOptionsDefaults ()=0
	Sets InitialWordOptionsDefaults.
virtual void	SetGappedExtensionDefaults ()=0
	Sets GappedExtensionDefaults.
virtual void	SetScoringOptionsDefaults ()=0
	Sets ScoringOptionsDefaults.
virtual void	SetHitSavingOptionsDefaults ()=0
	Sets HitSavingOptionsDefaults.
virtual void	SetEffectiveLengthsOptionsDefaults ()=0
	Sets EffectiveLengthsOptionsDefaults.
virtual void	SetSubjectSequenceOptionsDefaults ()=0
	Sets SubjectSequenceOptionsDefaults.
Protected Attributes
CRef< CBlastOptions >	m_Opts
	Data type this class controls access to.
bool	m_DefaultsMode
	Set to true when 'remote' options should ignore setters.

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Member Typedef Documentation

typedef CBlastOptions::EAPILocality CBlastOptionsHandle::EAPILocality

Convenience define. See also: CBlastOptions class Definition at line 145 of file blast_options_handle.hpp.

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Member Function Documentation

void CBlastOptionsHandle::ClearFilterOptions (   )  [inline]

Clears the filtering options. Definition at line 189 of file blast_options_handle.hpp. References m_Opts. Referenced by CBlastOptionsFactory::CreateTask().

void CBlastOptionsHandle::DoneDefaults (   )  [inline]

Returns true if this object needs default values set. Definition at line 175 of file blast_options_handle.hpp. References m_Opts.

int CBlastOptionsHandle::GetCullingLimit (   )  const [inline]

Returns Culling limit. Definition at line 267 of file blast_options_handle.hpp. References m_Opts. Referenced by BOOST_FIXTURE_TEST_CASE().

int CBlastOptionsHandle::GetCutoffScore (   )  const [inline]

Returns CutoffScore. Definition at line 243 of file blast_options_handle.hpp. References m_Opts. Referenced by BOOST_FIXTURE_TEST_CASE().

Int8 CBlastOptionsHandle::GetDbLength (   )  const [inline]

Returns DbLength. Definition at line 274 of file blast_options_handle.hpp. References m_Opts. Referenced by BOOST_FIXTURE_TEST_CASE().

unsigned int CBlastOptionsHandle::GetDbSeqNum (   )  const [inline]

Returns DbSeqNum. Definition at line 280 of file blast_options_handle.hpp. References m_Opts. Referenced by BOOST_FIXTURE_TEST_CASE().

Int8 CBlastOptionsHandle::GetEffectiveSearchSpace (   )  const [inline]

Returns EffectiveSearchSpace. Definition at line 286 of file blast_options_handle.hpp. References m_Opts. Referenced by BOOST_FIXTURE_TEST_CASE().

double CBlastOptionsHandle::GetEvalueThreshold (   )  const [inline]

Returns EvalueThreshold. Definition at line 238 of file blast_options_handle.hpp. References m_Opts. Referenced by BOOST_FIXTURE_TEST_CASE().

bool CBlastOptionsHandle::GetGappedMode (   )  const [inline]

Returns GappedMode. Definition at line 261 of file blast_options_handle.hpp. References m_Opts. Referenced by BOOST_FIXTURE_TEST_CASE().

double CBlastOptionsHandle::GetGapTrigger (   )  const [inline]

Returns GapTrigger. Definition at line 209 of file blast_options_handle.hpp. References m_Opts. Referenced by BOOST_FIXTURE_TEST_CASE().

double CBlastOptionsHandle::GetGapXDropoff (   )  const [inline]

Returns GapXDropoff. Definition at line 203 of file blast_options_handle.hpp. References m_Opts. Referenced by BOOST_FIXTURE_TEST_CASE().

double CBlastOptionsHandle::GetGapXDropoffFinal (   )  const [inline]

Returns GapXDropoffFinal. Definition at line 215 of file blast_options_handle.hpp. References m_Opts. Referenced by BOOST_FIXTURE_TEST_CASE().

int CBlastOptionsHandle::GetHitlistSize (   )  const [inline]

Returns HitlistSize. Definition at line 224 of file blast_options_handle.hpp. References m_Opts. Referenced by BOOST_FIXTURE_TEST_CASE().

bool CBlastOptionsHandle::GetMaskAtHash (   )  const [inline]

Returns whether masking should only be done for lookup table creation. Definition at line 197 of file blast_options_handle.hpp. References m_Opts. Referenced by BOOST_AUTO_TEST_CASE(), and BOOST_FIXTURE_TEST_CASE().

int CBlastOptionsHandle::GetMaxNumHspPerSequence (   )  const [inline]

Returns MaxNumHspPerSequence. Definition at line 230 of file blast_options_handle.hpp. References m_Opts. Referenced by BOOST_FIXTURE_TEST_CASE().

int CBlastOptionsHandle::GetMinDiagSeparation (   )  const [inline]

Returns MinDiagSeparation. Definition at line 255 of file blast_options_handle.hpp. References m_Opts.

int CBlastOptionsHandle::GetOffDiagonalRange (   )  const [inline]

Definition at line 184 of file blast_options_handle.hpp. References m_Opts.

const CBlastOptions& CBlastOptionsHandle::GetOptions (   )  const [inline]

Return the object which this object is a handle for. This method is intended to be used when one wants to INSPECT the values of options which are not exposed by the classes derived from CBlastOptionsHandle. Definition at line 159 of file blast_options_handle.hpp. References m_Opts. Referenced by Blast_FindWindowMaskerLoc_Fwd(), BOOST_AUTO_TEST_CASE(), CPsiBlastValidate::QueryFactory(), CBl2Seq::RunFullSearch(), CRedoAlignmentTestFixture::runRedoAlignmentCoreUnitTest(), and CRemoteBlast::x_Init().

double CBlastOptionsHandle::GetPercentIdentity (   )  const [inline]

Returns PercentIdentity. Definition at line 249 of file blast_options_handle.hpp. References m_Opts. Referenced by BOOST_FIXTURE_TEST_CASE().

int CBlastOptionsHandle::GetWindowSize (   )  const [inline]

Returns WindowSize. Definition at line 180 of file blast_options_handle.hpp. References m_Opts. Referenced by BOOST_FIXTURE_TEST_CASE().

void CBlastOptionsHandle::SetCullingLimit (  int  s  )  [inline]

Sets Culling limit. Parameters: s  CullingLimit [in] Definition at line 270 of file blast_options_handle.hpp. References m_Opts. Referenced by BOOST_FIXTURE_TEST_CASE().

void CBlastOptionsHandle::SetCutoffScore (  int  s  )  [inline]

Sets CutoffScore. Parameters: s  CutoffScore [in] Definition at line 246 of file blast_options_handle.hpp. References m_Opts. Referenced by BOOST_FIXTURE_TEST_CASE(), CBlastRPSOptionsHandle::SetHitSavingOptionsDefaults(), CBlastProteinOptionsHandle::SetHitSavingOptionsDefaults(), CBlastNucleotideOptionsHandle::SetHitSavingOptionsDefaults(), and CBlastNucleotideOptionsHandle::SetMBHitSavingOptionsDefaults().

void CBlastOptionsHandle::SetDbLength (  Int8  len  )  [inline]

Sets DbLength. Parameters: len  DbLength [in] Definition at line 277 of file blast_options_handle.hpp. References m_Opts. Referenced by BOOST_FIXTURE_TEST_CASE(), CBlastRPSOptionsHandle::SetEffectiveLengthsOptionsDefaults(), CBlastProteinOptionsHandle::SetEffectiveLengthsOptionsDefaults(), and CBlastNucleotideOptionsHandle::SetEffectiveLengthsOptionsDefaults().

void CBlastOptionsHandle::SetDbSeqNum (  unsigned int  num  )  [inline]

Sets DbSeqNum. Parameters: num  DbSeqNum [in] Definition at line 283 of file blast_options_handle.hpp. References m_Opts. Referenced by BOOST_FIXTURE_TEST_CASE(), CBlastRPSOptionsHandle::SetEffectiveLengthsOptionsDefaults(), CBlastProteinOptionsHandle::SetEffectiveLengthsOptionsDefaults(), and CBlastNucleotideOptionsHandle::SetEffectiveLengthsOptionsDefaults().

virtual void CBlastOptionsHandle::SetEffectiveLengthsOptionsDefaults (   )  [protected, pure virtual]

Sets EffectiveLengthsOptionsDefaults. Implemented in CBlastNucleotideOptionsHandle, CBlastProteinOptionsHandle, and CBlastRPSOptionsHandle. Referenced by SetDefaults().

void CBlastOptionsHandle::SetEffectiveSearchSpace (  Int8  eff  )  [inline]

Sets EffectiveSearchSpace. Parameters: eff  EffectiveSearchSpace [in] Definition at line 291 of file blast_options_handle.hpp. References m_Opts. Referenced by BOOST_FIXTURE_TEST_CASE(), CBlastRPSOptionsHandle::SetEffectiveLengthsOptionsDefaults(), CBlastProteinOptionsHandle::SetEffectiveLengthsOptionsDefaults(), and CBlastNucleotideOptionsHandle::SetEffectiveLengthsOptionsDefaults().

void CBlastOptionsHandle::SetEvalueThreshold (  double  eval  )  [inline]

Sets EvalueThreshold. Parameters: eval  EvalueThreshold [in] Definition at line 241 of file blast_options_handle.hpp. References m_Opts. Referenced by BOOST_AUTO_TEST_CASE(), BOOST_FIXTURE_TEST_CASE(), CBlastOptionsFactory::CreateTask(), DoSearchWordSize4(), s_CreateRepeatsSearchOptions(), CBlastRPSOptionsHandle::SetHitSavingOptionsDefaults(), CBlastProteinOptionsHandle::SetHitSavingOptionsDefaults(), CBlastNucleotideOptionsHandle::SetHitSavingOptionsDefaults(), and CBlastNucleotideOptionsHandle::SetMBHitSavingOptionsDefaults().

virtual void CBlastOptionsHandle::SetGappedExtensionDefaults (   )  [protected, pure virtual]

Sets GappedExtensionDefaults. Implemented in CBlastAdvancedProteinOptionsHandle, CBlastNucleotideOptionsHandle, CBlastProteinOptionsHandle, CBlastRPSOptionsHandle, CTBlastnOptionsHandle, and CTBlastxOptionsHandle. Referenced by SetDefaults().

void CBlastOptionsHandle::SetGappedMode (  bool  m = true  )  [inline]

Sets GappedMode. Parameters: m  GappedMode [in] Definition at line 264 of file blast_options_handle.hpp. References m_Opts. Referenced by BOOST_FIXTURE_TEST_CASE(), CBlastNucleotideOptionsHandle::SetMBScoringOptionsDefaults(), CBlastRPSOptionsHandle::SetScoringOptionsDefaults(), CBlastProteinOptionsHandle::SetScoringOptionsDefaults(), and CBlastNucleotideOptionsHandle::SetScoringOptionsDefaults().

void CBlastOptionsHandle::SetGapTrigger (  double  g  )  [inline]

Sets GapTrigger. Parameters: g  GapTrigger [in] Definition at line 212 of file blast_options_handle.hpp. References m_Opts. Referenced by BOOST_FIXTURE_TEST_CASE(), CBlastRPSOptionsHandle::SetGappedExtensionDefaults(), CBlastProteinOptionsHandle::SetGappedExtensionDefaults(), CBlastNucleotideOptionsHandle::SetGappedExtensionDefaults(), CDiscNucleotideOptionsHandle::SetMBGappedExtensionDefaults(), and CBlastNucleotideOptionsHandle::SetMBGappedExtensionDefaults().

void CBlastOptionsHandle::SetGapXDropoff (  double  x  )  [inline]

Sets GapXDropoff. Parameters: x  GapXDropoff [in] Definition at line 206 of file blast_options_handle.hpp. References m_Opts. Referenced by BOOST_AUTO_TEST_CASE(), BOOST_FIXTURE_TEST_CASE(), CBlastRPSOptionsHandle::SetGappedExtensionDefaults(), CBlastProteinOptionsHandle::SetGappedExtensionDefaults(), CBlastNucleotideOptionsHandle::SetGappedExtensionDefaults(), CDiscNucleotideOptionsHandle::SetMBGappedExtensionDefaults(), and CBlastNucleotideOptionsHandle::SetMBGappedExtensionDefaults().

void CBlastOptionsHandle::SetGapXDropoffFinal (  double  x  )  [inline]

Sets GapXDropoffFinal. Parameters: x  GapXDropoffFinal [in] Definition at line 220 of file blast_options_handle.hpp. References m_Opts. Referenced by BOOST_AUTO_TEST_CASE(), BOOST_FIXTURE_TEST_CASE(), s_CreateRepeatsSearchOptions(), CBlastRPSOptionsHandle::SetGappedExtensionDefaults(), CBlastProteinOptionsHandle::SetGappedExtensionDefaults(), CBlastNucleotideOptionsHandle::SetGappedExtensionDefaults(), CDiscNucleotideOptionsHandle::SetMBGappedExtensionDefaults(), and CBlastNucleotideOptionsHandle::SetMBGappedExtensionDefaults().

void CBlastOptionsHandle::SetHitlistSize (  int  s  )  [inline]

Sets HitlistSize. Parameters: s  HitlistSize [in] Definition at line 227 of file blast_options_handle.hpp. References m_Opts. Referenced by BOOST_FIXTURE_TEST_CASE(), CBlastRPSOptionsHandle::SetHitSavingOptionsDefaults(), CBlastProteinOptionsHandle::SetHitSavingOptionsDefaults(), CBlastNucleotideOptionsHandle::SetHitSavingOptionsDefaults(), and CBlastNucleotideOptionsHandle::SetMBHitSavingOptionsDefaults().

virtual void CBlastOptionsHandle::SetHitSavingOptionsDefaults (   )  [protected, pure virtual]

Sets HitSavingOptionsDefaults. Implemented in CBlastNucleotideOptionsHandle, CBlastProteinOptionsHandle, CBlastRPSOptionsHandle, CBlastxOptionsHandle, CTBlastnOptionsHandle, and CTBlastxOptionsHandle. Referenced by SetDefaults().

virtual void CBlastOptionsHandle::SetInitialWordOptionsDefaults (   )  [protected, pure virtual]

Sets InitialWordOptionsDefaults. Implemented in CBlastNucleotideOptionsHandle, CBlastProteinOptionsHandle, and CBlastRPSOptionsHandle. Referenced by SetDefaults().

virtual void CBlastOptionsHandle::SetLookupTableDefaults (   )  [protected, pure virtual]

Sets LookupTableDefaults. Implemented in CBlastNucleotideOptionsHandle, CBlastProteinOptionsHandle, CBlastRPSOptionsHandle, CBlastxOptionsHandle, CTBlastnOptionsHandle, and CTBlastxOptionsHandle. Referenced by SetDefaults().

void CBlastOptionsHandle::SetMaskAtHash (  bool  m = true  )  [inline]

Sets MaskAtHash. Parameters: m  whether masking should only be done for lookup table [in] Definition at line 200 of file blast_options_handle.hpp. References m_Opts. Referenced by BOOST_AUTO_TEST_CASE(), BOOST_FIXTURE_TEST_CASE(), and CBlastNucleotideOptionsHandle::SetQueryOptionDefaults().

void CBlastOptionsHandle::SetMaxNumHspPerSequence (  int  m  )  [inline]

Sets MaxNumHspPerSequence. Parameters: m  MaxNumHspPerSequence [in] Definition at line 235 of file blast_options_handle.hpp. References m_Opts. Referenced by BOOST_AUTO_TEST_CASE(), BOOST_FIXTURE_TEST_CASE(), CBlastRPSOptionsHandle::SetHitSavingOptionsDefaults(), CBlastProteinOptionsHandle::SetHitSavingOptionsDefaults(), CBlastNucleotideOptionsHandle::SetHitSavingOptionsDefaults(), and CBlastNucleotideOptionsHandle::SetMBHitSavingOptionsDefaults().

void CBlastOptionsHandle::SetMinDiagSeparation (  int  d  )  [inline]

Sets MinDiagSeparation. Parameters: d  MinDiagSeparation [in] Definition at line 258 of file blast_options_handle.hpp. References m_Opts. Referenced by CBlastRPSOptionsHandle::SetHitSavingOptionsDefaults(), CBlastProteinOptionsHandle::SetHitSavingOptionsDefaults(), CBlastNucleotideOptionsHandle::SetHitSavingOptionsDefaults(), and CBlastNucleotideOptionsHandle::SetMBHitSavingOptionsDefaults().

void CBlastOptionsHandle::SetOffDiagonalRange (  int  r  )  [inline]

Definition at line 185 of file blast_options_handle.hpp. References m_Opts. Referenced by CBlastNucleotideOptionsHandle::SetInitialWordOptionsDefaults().

CBlastOptions& CBlastOptionsHandle::SetOptions (   )  [inline]

Returns a reference to the internal options class which this object is a handle for. Please note that using objects of type CBlastOptions directly allows one to set inconsistent combinations of options. Note: Assumes user knows exactly how to set the individual options correctly. Calling CBlastOptions::Validate on this object is STRONGLY recommended. Definition at line 168 of file blast_options_handle.hpp. References m_Opts. Referenced by BOOST_AUTO_TEST_CASE(), CBlastOptionsFactory::CreateTask(), and CBlastOptionsBuilder::x_ApplyInteractions().

void CBlastOptionsHandle::SetPercentIdentity (  double  p  )  [inline]

Sets PercentIdentity. Parameters: p  PercentIdentity [in] Definition at line 252 of file blast_options_handle.hpp. References m_Opts. Referenced by BOOST_AUTO_TEST_CASE(), BOOST_FIXTURE_TEST_CASE(), CBlastRPSOptionsHandle::SetHitSavingOptionsDefaults(), CBlastProteinOptionsHandle::SetHitSavingOptionsDefaults(), CBlastNucleotideOptionsHandle::SetHitSavingOptionsDefaults(), and CBlastNucleotideOptionsHandle::SetMBHitSavingOptionsDefaults().

virtual void CBlastOptionsHandle::SetQueryOptionDefaults (   )  [protected, pure virtual]

Sets QueryOptionDefaults. Implemented in CBlastAdvancedProteinOptionsHandle, CBlastNucleotideOptionsHandle, CBlastProteinOptionsHandle, CBlastRPSOptionsHandle, CBlastxOptionsHandle, CPSIBlastOptionsHandle, CRPSTBlastnOptionsHandle, and CTBlastxOptionsHandle. Referenced by SetDefaults().

virtual void CBlastOptionsHandle::SetRemoteProgramAndService_Blast3 (   )  [protected, pure virtual]

Set the program and service name for remote blast. Implemented in CBlastNucleotideOptionsHandle, CBlastProteinOptionsHandle, CBlastRPSOptionsHandle, CBlastxOptionsHandle, CDiscNucleotideOptionsHandle, CPSIBlastOptionsHandle, CRPSTBlastnOptionsHandle, CTBlastnOptionsHandle, and CTBlastxOptionsHandle.

virtual void CBlastOptionsHandle::SetScoringOptionsDefaults (   )  [protected, pure virtual]

Sets ScoringOptionsDefaults. Implemented in CBlastNucleotideOptionsHandle, CBlastProteinOptionsHandle, CBlastRPSOptionsHandle, CBlastxOptionsHandle, CTBlastnOptionsHandle, and CTBlastxOptionsHandle. Referenced by SetDefaults().

virtual void CBlastOptionsHandle::SetSubjectSequenceOptionsDefaults (   )  [protected, pure virtual]

Sets SubjectSequenceOptionsDefaults. Implemented in CBlastNucleotideOptionsHandle, CBlastProteinOptionsHandle, CBlastRPSOptionsHandle, CTBlastnOptionsHandle, and CTBlastxOptionsHandle. Referenced by SetDefaults().

void CBlastOptionsHandle::SetWindowSize (  int  ws  )  [inline]

Sets WindowSize. Parameters: ws  WindowSize [in] Definition at line 183 of file blast_options_handle.hpp. References m_Opts. Referenced by BOOST_AUTO_TEST_CASE(), BOOST_FIXTURE_TEST_CASE(), CBlastRPSOptionsHandle::SetInitialWordOptionsDefaults(), CBlastProteinOptionsHandle::SetInitialWordOptionsDefaults(), CBlastNucleotideOptionsHandle::SetInitialWordOptionsDefaults(), CDiscNucleotideOptionsHandle::SetMBInitialWordOptionsDefaults(), and CBlastNucleotideOptionsHandle::SetMBInitialWordOptionsDefaults().

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Member Data Documentation

bool CBlastOptionsHandle::m_DefaultsMode [protected]

Set to true when 'remote' options should ignore setters. Definition at line 303 of file blast_options_handle.hpp.

CRef<CBlastOptions> CBlastOptionsHandle::m_Opts [protected]

Data type this class controls access to. Definition at line 300 of file blast_options_handle.hpp. Referenced by ClearFilterOptions(), DoneDefaults(), GetCullingLimit(), GetCutoffScore(), GetDbLength(), GetDbSeqNum(), GetEffectiveSearchSpace(), GetEvalueThreshold(), GetFilterString(), GetGappedMode(), GetGapTrigger(), GetGapXDropoff(), GetGapXDropoffFinal(), GetHitlistSize(), GetMaskAtHash(), GetMaxNumHspPerSequence(), GetMinDiagSeparation(), GetOffDiagonalRange(), GetOptions(), GetPercentIdentity(), CPHIBlastProtOptionsHandle::GetPHIPattern(), CPHIBlastNuclOptionsHandle::GetPHIPattern(), GetWindowSize(), SetCullingLimit(), SetCutoffScore(), SetDbLength(), SetDbSeqNum(), SetDefaults(), CBlastNucleotideOptionsHandle::SetDefaults(), SetEffectiveSearchSpace(), SetEvalueThreshold(), SetFilterString(), CTBlastxOptionsHandle::SetGappedExtensionDefaults(), CTBlastnOptionsHandle::SetGappedExtensionDefaults(), CBlastRPSOptionsHandle::SetGappedExtensionDefaults(), CBlastProteinOptionsHandle::SetGappedExtensionDefaults(), CBlastAdvancedProteinOptionsHandle::SetGappedExtensionDefaults(), SetGappedMode(), SetGapTrigger(), SetGapXDropoff(), SetGapXDropoffFinal(), SetHitlistSize(), CTBlastxOptionsHandle::SetHitSavingOptionsDefaults(), CTBlastnOptionsHandle::SetHitSavingOptionsDefaults(), CBlastxOptionsHandle::SetHitSavingOptionsDefaults(), CBlastRPSOptionsHandle::SetHitSavingOptionsDefaults(), CTBlastxOptionsHandle::SetLookupTableDefaults(), CBlastxOptionsHandle::SetLookupTableDefaults(), CBlastRPSOptionsHandle::SetLookupTableDefaults(), CBlastProteinOptionsHandle::SetLookupTableDefaults(), CBlastNucleotideOptionsHandle::SetLookupTableDefaults(), SetMaskAtHash(), SetMaxNumHspPerSequence(), CDiscNucleotideOptionsHandle::SetMBInitialWordOptionsDefaults(), CDiscNucleotideOptionsHandle::SetMBLookupTableDefaults(), CBlastNucleotideOptionsHandle::SetMBLookupTableDefaults(), CBlastNucleotideOptionsHandle::SetMBScoringOptionsDefaults(), SetMinDiagSeparation(), SetOffDiagonalRange(), SetOptions(), SetPercentIdentity(), CPHIBlastProtOptionsHandle::SetPHIPattern(), CPHIBlastNuclOptionsHandle::SetPHIPattern(), CPSIBlastOptionsHandle::SetPSIBlastDefaults(), CPSIBlastOptionsHandle::SetPSITblastnDefaults(), CTBlastxOptionsHandle::SetQueryOptionDefaults(), CRPSTBlastnOptionsHandle::SetQueryOptionDefaults(), CPSIBlastOptionsHandle::SetQueryOptionDefaults(), CBlastxOptionsHandle::SetQueryOptionDefaults(), CBlastRPSOptionsHandle::SetQueryOptionDefaults(), CBlastProteinOptionsHandle::SetQueryOptionDefaults(), CTBlastxOptionsHandle::SetScoringOptionsDefaults(), CBlastRPSOptionsHandle::SetScoringOptionsDefaults(), CBlastProteinOptionsHandle::SetScoringOptionsDefaults(), CBlastNucleotideOptionsHandle::SetScoringOptionsDefaults(), CTBlastxOptionsHandle::SetSubjectSequenceOptionsDefaults(), CBlastNucleotideOptionsHandle::SetTraditionalBlastnDefaults(), CBlastNucleotideOptionsHandle::SetTraditionalMegablastDefaults(), SetWindowSize(), and Validate().

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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

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