NCBI C++ ToolKit
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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 CAtomicCounter TCounter
 Counter type is CAtomiCounter. More...
 
typedef TCounter::TValue 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< CBlastOptionsClone () 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)
 
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...
 
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)
 
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)
 
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
 
TBlast4OptsGetBlast4AlgoOpts ()
 
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 CBlastOptionsMementoCreateSnapshot () 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...
 
CObjectoperator= (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 Member Functions

 CBlastOptions (const CBlastOptions &bo)
 Prohibit copy c-tor. More...
 
CBlastOptionsoperator= (const CBlastOptions &bo)
 Prohibit assignment operator. More...
 
void x_Throwx (const string &msg) const
 Auxiliary to throw CBlastExceptions. More...
 
QuerySetUpOptionsGetQueryOpts () const
 Returns QuerySetUpOptions for eLocal objects, NULL for eRemote. More...
 
LookupTableOptionsGetLutOpts () const
 Returns LookupTableOptions for eLocal objects, NULL for eRemote. More...
 
BlastInitialWordOptionsGetInitWordOpts () const
 Returns BlastInitialWordOptions for eLocal objects, NULL for eRemote. More...
 
BlastExtensionOptionsGetExtnOpts () const
 Returns BlastExtensionOptions for eLocal objects, NULL for eRemote. More...
 
BlastHitSavingOptionsGetHitSaveOpts () const
 Returns BlastHitSavingOptions for eLocal objects, NULL for eRemote. More...
 
PSIBlastOptionsGetPSIBlastOpts () const
 Returns PSIBlastOptions for eLocal objects, NULL for eRemote. More...
 
BlastDatabaseOptionsGetDbOpts () const
 Returns BlastDatabaseOptions for eLocal objects, NULL for eRemote. More...
 
BlastScoringOptionsGetScoringOpts () const
 Returns BlastScoringOptions for eLocal objects, NULL for eRemote. More...
 
BlastEffectiveLengthsOptionsGetEffLenOpts () const
 Returns BlastEffectiveLengthsOptions for eLocal objects, NULL for eRemote. More...
 
void x_DoDeepCopy (const CBlastOptions &opts)
 Perform a "deep copy" of Blast options. More...
 

Private Attributes

CBlastOptionsLocalm_Local
 
CBlastOptionsRemotem_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_NORETURN void ThrowNullPointerException (void)
 Define method to throw null pointer exception. More...
 
static NCBI_NORETURN 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

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

This returns a list of parameters for remote searches.

Definition at line 439 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
inlinevirtual

Get the program and service name for remote blast.

Definition at line 455 of file blast_options.hpp.

References _ASSERT.

Referenced by BOOST_AUTO_TEST_CASE(), CRemoteBlast::x_Init(), and CExportStrategy::x_Process_BlastOptions().

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

Prohibit assignment operator.

void CBlastOptions::SetRemoteProgramAndService_Blast3 ( const string p,
const string s 
)
inline

Friends And Related Function Documentation

friend class ::CBlastSetupTestFixture
friend

Definition at line 533 of file blast_options.hpp.

friend class ::CBlastTabularFormatThread
friend

Definition at line 529 of file blast_options.hpp.

friend class ::CTracebackSearchTestFixture
friend

Definition at line 535 of file blast_options.hpp.

friend class ::CTracebackTestFixture
friend

Definition at line 532 of file blast_options.hpp.

friend class ::CUniformSearchTest
friend

Definition at line 534 of file blast_options.hpp.

friend class CBl2Seq
friend

Definition at line 521 of file blast_options.hpp.

friend class CDbBlast
friend

Definition at line 522 of file blast_options.hpp.

friend class CDbBlastPrelim
friend

Definition at line 524 of file blast_options.hpp.

friend class CDbBlastTraceback
friend

Definition at line 523 of file blast_options.hpp.

friend class CEffectiveSearchSpacesMemento
friend

Definition at line 525 of file blast_options.hpp.

Member Data Documentation

bool CBlastOptions::m_DefaultsMode
private

Defaults mode (remote options will ignore Set ops).

Definition at line 488 of file blast_options.hpp.

Referenced by x_DoDeepCopy().

CAutomaticGenCodeSingleton CBlastOptions::m_GenCodeSingletonVar
private

This field is add.

Definition at line 519 of file blast_options.hpp.

Referenced by SetDbGeneticCode(), and SetQueryGeneticCode().

CBlastOptionsLocal* CBlastOptions::m_Local
private

Definition at line 478 of file blast_options.hpp.

Referenced by CBlastOptions(), CEffectiveSearchSpacesMemento::CEffectiveSearchSpacesMemento(), CreateSnapshot(), DebugDump(), GetBestHitOverhang(), GetBestHitScoreEdge(), GetComplexityAdjMode(), GetCompositionBasedStats(), GetCullingLimit(), GetCutoffScore(), 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(), GetMaxHspsPerSubject(), GetMaxMismatches(), GetMaxNumHspPerSequence(), GetMBIndexLoaded(), GetMBTemplateLength(), GetMBTemplateType(), GetMinDiagSeparation(), GetMismatchPenalty(), GetMismatchWindow(), GetOffDiagonalRange(), GetOutOfFrameMode(), GetPaired(), GetPercentIdentity(), GetPHIPattern(), GetProgram(), GetProgramType(), GetPseudoCount(), GetPSIBlastOpts(), GetQueryCovHspPerc(), GetQueryGeneticCode(), GetQueryOpts(), GetRepeatFiltering(), GetRepeatFilteringDB(), GetScoringOpts(), GetSegFiltering(), GetSegFilteringHicut(), GetSegFilteringLocut(), GetSegFilteringWindow(), GetSmithWatermanMode(), GetSpliceAlignments(), GetStrandOption(), GetSumStatisticsMode(), GetUnifiedP(), GetUseIndex(), GetWindowMaskerDatabase(), GetWindowMaskerTaxId(), GetWindowSize(), GetWordSize(), GetWordThreshold(), GetXDropoff(), operator==(), SetBestHitOverhang(), SetBestHitScoreEdge(), SetComplexityAdjMode(), SetCompositionBasedStats(), SetCullingLimit(), SetCutoffScore(), 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(), SetMaxHspsPerSubject(), SetMaxMismatches(), SetMaxNumHspPerSequence(), SetMBIndexLoaded(), SetMBTemplateLength(), SetMBTemplateType(), SetMinDiagSeparation(), SetMismatchPenalty(), SetMismatchWindow(), SetOffDiagonalRange(), SetOutOfFrameMode(), SetPaired(), SetPercentIdentity(), SetPHIPattern(), SetProgram(), SetPseudoCount(), SetQueryCovHspPerc(), SetQueryGeneticCode(), SetRepeatFiltering(), SetRepeatFilteringDB(), SetSegFiltering(), SetSegFilteringHicut(), SetSegFilteringLocut(), SetSegFilteringWindow(), SetSmithWatermanMode(), SetSpliceAlignments(), 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 482 of file blast_options.hpp.

Referenced by x_DoDeepCopy().

CBlastOptionsRemote* CBlastOptions::m_Remote
private

Definition at line 479 of file blast_options.hpp.

Referenced by CBlastOptions(), DoneDefaults(), GetBlast4AlgoOpts(), GetDefaultsMode(), GetLocality(), 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(), SetMaxHspsPerSubject(), SetMaxNumHspPerSequence(), SetMBTemplateLength(), SetMBTemplateType(), SetMismatchPenalty(), SetOutOfFrameMode(), SetPercentIdentity(), SetPHIPattern(), SetProgram(), SetPseudoCount(), SetQueryCovHspPerc(), 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 485 of file blast_options.hpp.

Referenced by x_DoDeepCopy().


The documentation for this class was generated from the following files:
Modified on Thu Mar 30 17:12:52 2017 by modify_doxy.py rev. 506947