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

Search Toolkit Book for CBlastOptions

#include <blast_options.hpp>

Inheritance diagram for CBlastOptions:

[legend]Collaboration diagram for CBlastOptions:

[legend]List of all members.

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 86 of file blast_options.hpp.

Public Types

typedef ncbi::objects::CBlast4_parameters TBlast4Opts

This returns a list of parameters for remote searches.

enum EAPILocality { eLocal, eRemote, eBoth }

Enumerates the possible contexts in which objects of this type can be used. 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).

~CBlastOptions ()

Destructor.

CRef< CBlastOptions > Clone () const

Explicit deep copy of the Blast options object.

EAPILocality GetLocality () const

Return the locality used when the object was created.

bool Validate () const

Validate the options.

EProgram GetProgram () const

Returns the task this object is best suited for.

void SetProgram (EProgram p)

Sets the task this object is best suited for.

EBlastProgramType GetProgramType () const

Returns the CORE BLAST notion of program type.

double GetWordThreshold () const

Returns WordThreshold.

void SetWordThreshold (double w)

Sets WordThreshold.

ELookupTableType GetLookupTableType () const

void SetLookupTableType (ELookupTableType type)

int GetWordSize () const

void SetWordSize (int ws)

unsigned char GetMBTemplateLength () const

Megablast only lookup table options.

void SetMBTemplateLength (unsigned char len)

unsigned char GetMBTemplateType () const

void SetMBTemplateType (unsigned char type)

void ClearFilterOptions ()

NCBI_DEPRECATED char * GetFilterString () const

Return the filtering string used.

NCBI_DEPRECATED 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.

void SetRepeatFiltering (bool val=true)

Turns on repeat filtering using the default repeat database, namely kDefaultRepeatFilterDb.

const char * GetRepeatFilteringDB () const

Returns the name of the repeat filtering database to use.

void SetRepeatFilteringDB (const char *db)

Sets the repeat filtering database to use.

int GetWindowMaskerTaxId () const

Returns the tax id used for the windowmasker database to use, if set via SetWindowMaskerTaxId (otherwise, returns 0).

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.

const char * GetWindowMaskerDatabase () const

Return the name of the windowmasker database to use.

void SetWindowMaskerDatabase (const char *db)

Sets the windowmasker database to use.

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 GetHitlistSize () const

void SetHitlistSize (int s)

int GetMaxNumHspPerSequence () const

void SetMaxNumHspPerSequence (int m)

int GetCullingLimit () const

void SetCullingLimit (int s)

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)

double GetPercentIdentity () const

void SetPercentIdentity (double p)

int GetMinDiagSeparation () const

void SetMinDiagSeparation (int d)

bool GetSumStatisticsMode () const

Sum statistics options.

void SetSumStatisticsMode (bool m=true)

int GetLongestIntronLength () const

for linking HSPs with uneven gaps

void SetLongestIntronLength (int l)

for linking HSPs with uneven gaps

bool GetGappedMode () const

Returns true if gapped BLAST is set, false otherwise.

void SetGappedMode (bool m=true)

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 GetUseIndex () const

bool GetForceIndex () 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)

void DebugDump (CDebugDumpContext ddc, unsigned int depth) const

Allows to dump a snapshot of the object.

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.

virtual void GetRemoteProgramAndService_Blast3 (string &p, string &s) const

Get the program and service name for remote blast.

const CBlastOptionsMemento * CreateSnapshot () const

Create a snapshot of the state of this object for internal use of its data structures (BLAST C++ APIs only).

void SetDefaultsMode (bool dmode)

If this is true, remote options will ignore "Set" calls.

bool GetDefaultsMode () const

Private Member Functions

CBlastOptions (const CBlastOptions &bo)

Prohibit copy c-tor.

CBlastOptions & operator= (const CBlastOptions &bo)

Prohibit assignment operator.

void x_Throwx (const string &msg) const

Auxiliary to throw CBlastExceptions.

QuerySetUpOptions * GetQueryOpts () const

Returns QuerySetUpOptions for eLocal objects, NULL for eRemote.

LookupTableOptions * GetLutOpts () const

Returns LookupTableOptions for eLocal objects, NULL for eRemote.

BlastInitialWordOptions * GetInitWordOpts () const

Returns BlastInitialWordOptions for eLocal objects, NULL for eRemote.

BlastExtensionOptions * GetExtnOpts () const

Returns BlastExtensionOptions for eLocal objects, NULL for eRemote.

BlastHitSavingOptions * GetHitSaveOpts () const

Returns BlastHitSavingOptions for eLocal objects, NULL for eRemote.

PSIBlastOptions * GetPSIBlastOpts () const

Returns PSIBlastOptions for eLocal objects, NULL for eRemote.

BlastDatabaseOptions * GetDbOpts () const

Returns BlastDatabaseOptions for eLocal objects, NULL for eRemote.

BlastScoringOptions * GetScoringOpts () const

Returns BlastScoringOptions for eLocal objects, NULL for eRemote.

BlastEffectiveLengthsOptions * GetEffLenOpts () const

Returns BlastEffectiveLengthsOptions for eLocal objects, NULL for eRemote.

void x_DoDeepCopy (const CBlastOptions &opts)

Perform a "deep copy" of Blast options.

Private Attributes

CBlastOptionsLocal * m_Local

CBlastOptionsRemote * m_Remote

string m_ProgramName

Program Name for Blast3.

string m_ServiceName

Service Name for Blast3.

bool m_DefaultsMode

Defaults mode (remote options will ignore Set ops).

CAutomaticGenCodeSingleton m_GenCodeSingletonVar

This field is add.

Friends

class CBl2Seq

class CDbBlast

class CDbBlastTraceback

class CDbBlastPrelim

class CEffectiveSearchSpacesMemento

class ::CBlastTabularFormatThread

class ::CTracebackTestFixture

class ::CBlastSetupTestFixture

class ::CUniformSearchTest

class ::CTracebackSearchTestFixture

Member Typedef Documentation

typedef ncbi::objects::CBlast4_parameters CBlastOptions::TBlast4Opts

This returns a list of parameters for remote searches.

Definition at line 387 of file blast_options.hpp.

Member Enumeration Documentation

enum CBlastOptions::EAPILocality

Enumerates the possible contexts in which objects of this type can be used.

Enumerator:

eLocal To be used for running BLAST locally.

See also:
CBl2Seq, CLocalBlast

eRemote To be used when running BLAST remotely.

See also:
CRemoteBlast

eBoth

Definition at line 91 of file blast_options.hpp.

Constructor & Destructor Documentation

CBlastOptions::CBlastOptions ( const CBlastOptions & bo ) [private]

Prohibit copy c-tor.

Member Function Documentation

virtual void CBlastOptions::GetRemoteProgramAndService_Blast3 ( string & p,

string & s

) const [inline, virtual]

Get the program and service name for remote blast.

Definition at line 403 of file blast_options.hpp.
References _ASSERT.
Referenced by CRemoteBlast::x_Init().

CBlastOptions& CBlastOptions::operator= ( const CBlastOptions & bo ) [private]

Prohibit assignment operator.

void CBlastOptions::SetRemoteProgramAndService_Blast3 ( const string & p,

const string & s

) [inline]

Set the program and service name for remote blast.

Definition at line 396 of file blast_options.hpp.

Friends And Related Function Documentation

friend class ::CBlastSetupTestFixture [friend]

Definition at line 481 of file blast_options.hpp.

friend class ::CBlastTabularFormatThread [friend]

Definition at line 477 of file blast_options.hpp.

friend class ::CTracebackSearchTestFixture [friend]

Definition at line 483 of file blast_options.hpp.

friend class ::CTracebackTestFixture [friend]

Definition at line 480 of file blast_options.hpp.

friend class ::CUniformSearchTest [friend]

Definition at line 482 of file blast_options.hpp.

friend class CBl2Seq [friend]

Definition at line 469 of file blast_options.hpp.

friend class CDbBlast [friend]

Definition at line 470 of file blast_options.hpp.

friend class CDbBlastPrelim [friend]

Definition at line 472 of file blast_options.hpp.

friend class CDbBlastTraceback [friend]

Definition at line 471 of file blast_options.hpp.

friend class CEffectiveSearchSpacesMemento [friend]

Definition at line 473 of file blast_options.hpp.

Member Data Documentation

bool CBlastOptions::m_DefaultsMode [private]

Defaults mode (remote options will ignore Set ops).

Definition at line 436 of file blast_options.hpp.
Referenced by x_DoDeepCopy().

CAutomaticGenCodeSingleton CBlastOptions::m_GenCodeSingletonVar [private]

This field is add.

Definition at line 467 of file blast_options.hpp.

CBlastOptionsLocal* CBlastOptions::m_Local [private]

Definition at line 426 of file blast_options.hpp.
Referenced by CBlastOptions(), CEffectiveSearchSpacesMemento::CEffectiveSearchSpacesMemento(), CreateSnapshot(), DebugDump(), GetBestHitOverhang(), GetBestHitScoreEdge(), GetCompositionBasedStats(), GetCullingLimit(), GetCutoffScore(), GetDbGeneticCode(), GetDbLength(), GetDbOpts(), GetDbSeqNum(), GetDustFiltering(), GetDustFilteringLevel(), GetDustFilteringLinker(), GetDustFilteringWindow(), GetEffectiveSearchSpace(), GetEffLenOpts(), GetEvalueThreshold(), GetExtnOpts(), GetFilterString(), GetForceIndex(), GetFrameShiftPenalty(), GetGapExtensionCost(), GetGapExtnAlgorithm(), GetGapOpeningCost(), GetGappedMode(), GetGapTracebackAlgorithm(), GetGapTrigger(), GetGapXDropoff(), GetGapXDropoffFinal(), GetHitlistSize(), GetHitSaveOpts(), GetInclusionThreshold(), GetIndexName(), GetInitWordOpts(), GetLocality(), GetLongestIntronLength(), GetLookupTableType(), GetLutOpts(), GetMaskAtHash(), GetMatchReward(), GetMatrixName(), GetMaxNumHspPerSequence(), GetMBIndexLoaded(), GetMBTemplateLength(), GetMBTemplateType(), GetMinDiagSeparation(), GetMismatchPenalty(), GetOffDiagonalRange(), GetOutOfFrameMode(), GetPercentIdentity(), GetPHIPattern(), GetProgram(), GetProgramType(), GetPseudoCount(), GetPSIBlastOpts(), GetQueryGeneticCode(), GetQueryOpts(), GetRepeatFiltering(), GetRepeatFilteringDB(), GetScoringOpts(), GetSegFiltering(), GetSegFilteringHicut(), GetSegFilteringLocut(), GetSegFilteringWindow(), GetSmithWatermanMode(), GetStrandOption(), GetSumStatisticsMode(), GetUnifiedP(), GetUseIndex(), GetWindowMaskerDatabase(), GetWindowMaskerTaxId(), GetWindowSize(), GetWordSize(), GetWordThreshold(), GetXDropoff(), operator==(), SetBestHitOverhang(), SetBestHitScoreEdge(), SetCompositionBasedStats(), SetCullingLimit(), SetCutoffScore(), SetDbGeneticCode(), SetDbLength(), SetDbSeqNum(), SetDustFiltering(), SetDustFilteringLevel(), SetDustFilteringLinker(), SetDustFilteringWindow(), SetEffectiveSearchSpace(), SetEvalueThreshold(), SetFilterString(), SetFrameShiftPenalty(), SetGapExtensionCost(), SetGapExtnAlgorithm(), SetGapOpeningCost(), SetGappedMode(), SetGapTracebackAlgorithm(), SetGapTrigger(), SetGapXDropoff(), SetGapXDropoffFinal(), SetHitlistSize(), SetInclusionThreshold(), SetLongestIntronLength(), SetLookupTableType(), SetMaskAtHash(), SetMatchReward(), SetMatrixName(), SetMaxNumHspPerSequence(), SetMBIndexLoaded(), SetMBTemplateLength(), SetMBTemplateType(), SetMinDiagSeparation(), SetMismatchPenalty(), SetOffDiagonalRange(), SetOutOfFrameMode(), SetPercentIdentity(), SetPHIPattern(), SetProgram(), SetPseudoCount(), SetQueryGeneticCode(), SetRepeatFiltering(), SetRepeatFilteringDB(), SetSegFiltering(), SetSegFilteringHicut(), SetSegFilteringLocut(), SetSegFilteringWindow(), SetSmithWatermanMode(), SetStrandOption(), SetSumStatisticsMode(), SetUnifiedP(), SetUseIndex(), SetWindowMaskerDatabase(), SetWindowMaskerTaxId(), SetWindowSize(), SetWordSize(), SetWordThreshold(), SetXDropoff(), Validate(), x_DoDeepCopy(), ~CBlastOptions(), and CEffectiveSearchSpacesMemento::~CEffectiveSearchSpacesMemento().

string CBlastOptions::m_ProgramName [private]

Program Name for Blast3.

Definition at line 430 of file blast_options.hpp.
Referenced by x_DoDeepCopy().

CBlastOptionsRemote* CBlastOptions::m_Remote [private]

Definition at line 427 of file blast_options.hpp.
Referenced by CBlastOptions(), DoneDefaults(), GetBlast4AlgoOpts(), GetDefaultsMode(), GetLocality(), SetBestHitOverhang(), SetBestHitScoreEdge(), SetCompositionBasedStats(), SetCullingLimit(), SetCutoffScore(), SetDbGeneticCode(), SetDbLength(), SetDbSeqNum(), SetDefaultsMode(), SetDustFiltering(), SetDustFilteringLevel(), SetDustFilteringLinker(), SetDustFilteringWindow(), SetEffectiveSearchSpace(), SetEvalueThreshold(), SetFilterString(), SetFrameShiftPenalty(), SetGapExtensionCost(), SetGapExtnAlgorithm(), SetGapOpeningCost(), SetGappedMode(), SetGapTracebackAlgorithm(), SetGapTrigger(), SetGapXDropoff(), SetGapXDropoffFinal(), SetHitlistSize(), SetInclusionThreshold(), SetLongestIntronLength(), SetLookupTableType(), SetMaskAtHash(), SetMatchReward(), SetMatrixName(), SetMaxNumHspPerSequence(), SetMBTemplateLength(), SetMBTemplateType(), SetMismatchPenalty(), SetOutOfFrameMode(), SetPercentIdentity(), SetPHIPattern(), SetProgram(), SetPseudoCount(), SetQueryGeneticCode(), SetRepeatFiltering(), SetRepeatFilteringDB(), SetSegFiltering(), SetSegFilteringHicut(), SetSegFilteringLocut(), SetSegFilteringWindow(), SetSmithWatermanMode(), SetStrandOption(), SetSumStatisticsMode(), SetUnifiedP(), SetUseIndex(), SetWindowMaskerDatabase(), SetWindowMaskerTaxId(), SetWindowSize(), SetWordSize(), SetWordThreshold(), SetXDropoff(), x_DoDeepCopy(), and ~CBlastOptions().

string CBlastOptions::m_ServiceName [private]

Service Name for Blast3.

Definition at line 433 of file blast_options.hpp.
Referenced by 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

Generated on Mon Dec 7 10:28:41 2009 for NCBI C++ ToolKit by

1.4.6

Modified on Mon Dec 07 16:22:44 2009 by modify_doxy.py rev. 173732


Public Types
typedef ncbi::objects::CBlast4_parameters	TBlast4Opts
	This returns a list of parameters for remote searches.
enum	EAPILocality { eLocal, eRemote, eBoth }
	Enumerates the possible contexts in which objects of this type can be used. 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).
	~CBlastOptions ()
	Destructor.
CRef< CBlastOptions >	Clone () const
	Explicit deep copy of the Blast options object.
EAPILocality	GetLocality () const
	Return the locality used when the object was created.
bool	Validate () const
	Validate the options.
EProgram	GetProgram () const
	Returns the task this object is best suited for.
void	SetProgram (EProgram p)
	Sets the task this object is best suited for.
EBlastProgramType	GetProgramType () const
	Returns the CORE BLAST notion of program type.
double	GetWordThreshold () const
	Returns WordThreshold.
void	SetWordThreshold (double w)
	Sets WordThreshold.
ELookupTableType	GetLookupTableType () const
void	SetLookupTableType (ELookupTableType type)
int	GetWordSize () const
void	SetWordSize (int ws)
unsigned char	GetMBTemplateLength () const
	Megablast only lookup table options.
void	SetMBTemplateLength (unsigned char len)
unsigned char	GetMBTemplateType () const
void	SetMBTemplateType (unsigned char type)
void	ClearFilterOptions ()
NCBI_DEPRECATED char *	GetFilterString () const
	Return the filtering string used.
NCBI_DEPRECATED 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.
void	SetRepeatFiltering (bool val=true)
	Turns on repeat filtering using the default repeat database, namely kDefaultRepeatFilterDb.
const char *	GetRepeatFilteringDB () const
	Returns the name of the repeat filtering database to use.
void	SetRepeatFilteringDB (const char *db)
	Sets the repeat filtering database to use.
int	GetWindowMaskerTaxId () const
	Returns the tax id used for the windowmasker database to use, if set via SetWindowMaskerTaxId (otherwise, returns 0).
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.
const char *	GetWindowMaskerDatabase () const
	Return the name of the windowmasker database to use.
void	SetWindowMaskerDatabase (const char *db)
	Sets the windowmasker database to use.
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	GetHitlistSize () const
void	SetHitlistSize (int s)
int	GetMaxNumHspPerSequence () const
void	SetMaxNumHspPerSequence (int m)
int	GetCullingLimit () const
void	SetCullingLimit (int s)
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)
double	GetPercentIdentity () const
void	SetPercentIdentity (double p)
int	GetMinDiagSeparation () const
void	SetMinDiagSeparation (int d)
bool	GetSumStatisticsMode () const
	Sum statistics options.
void	SetSumStatisticsMode (bool m=true)
int	GetLongestIntronLength () const
	for linking HSPs with uneven gaps
void	SetLongestIntronLength (int l)
	for linking HSPs with uneven gaps
bool	GetGappedMode () const
	Returns true if gapped BLAST is set, false otherwise.
void	SetGappedMode (bool m=true)
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	GetUseIndex () const
bool	GetForceIndex () 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)
void	DebugDump (CDebugDumpContext ddc, unsigned int depth) const
	Allows to dump a snapshot of the object.
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.
virtual void	GetRemoteProgramAndService_Blast3 (string &p, string &s) const
	Get the program and service name for remote blast.
const CBlastOptionsMemento *	CreateSnapshot () const
	Create a snapshot of the state of this object for internal use of its data structures (BLAST C++ APIs only).
void	SetDefaultsMode (bool dmode)
	If this is true, remote options will ignore "Set" calls.
bool	GetDefaultsMode () const
Private Member Functions
	CBlastOptions (const CBlastOptions &bo)
	Prohibit copy c-tor.
CBlastOptions &	operator= (const CBlastOptions &bo)
	Prohibit assignment operator.
void	x_Throwx (const string &msg) const
	Auxiliary to throw CBlastExceptions.
QuerySetUpOptions *	GetQueryOpts () const
	Returns QuerySetUpOptions for eLocal objects, NULL for eRemote.
LookupTableOptions *	GetLutOpts () const
	Returns LookupTableOptions for eLocal objects, NULL for eRemote.
BlastInitialWordOptions *	GetInitWordOpts () const
	Returns BlastInitialWordOptions for eLocal objects, NULL for eRemote.
BlastExtensionOptions *	GetExtnOpts () const
	Returns BlastExtensionOptions for eLocal objects, NULL for eRemote.
BlastHitSavingOptions *	GetHitSaveOpts () const
	Returns BlastHitSavingOptions for eLocal objects, NULL for eRemote.
PSIBlastOptions *	GetPSIBlastOpts () const
	Returns PSIBlastOptions for eLocal objects, NULL for eRemote.
BlastDatabaseOptions *	GetDbOpts () const
	Returns BlastDatabaseOptions for eLocal objects, NULL for eRemote.
BlastScoringOptions *	GetScoringOpts () const
	Returns BlastScoringOptions for eLocal objects, NULL for eRemote.
BlastEffectiveLengthsOptions *	GetEffLenOpts () const
	Returns BlastEffectiveLengthsOptions for eLocal objects, NULL for eRemote.
void	x_DoDeepCopy (const CBlastOptions &opts)
	Perform a "deep copy" of Blast options.
Private Attributes
CBlastOptionsLocal *	m_Local
CBlastOptionsRemote *	m_Remote
string	m_ProgramName
	Program Name for Blast3.
string	m_ServiceName
	Service Name for Blast3.
bool	m_DefaultsMode
	Defaults mode (remote options will ignore Set ops).
CAutomaticGenCodeSingleton	m_GenCodeSingletonVar
	This field is add.
Friends
class	CBl2Seq
class	CDbBlast
class	CDbBlastTraceback
class	CDbBlastPrelim
class	CEffectiveSearchSpacesMemento
class	::CBlastTabularFormatThread
class	::CTracebackTestFixture
class	::CBlastSetupTestFixture
class	::CUniformSearchTest
class	::CTracebackSearchTestFixture

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

Detailed Description

Public Types

Public Member Functions

Private Member Functions

Private Attributes