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NCBI C++ ToolKit: include/algo/blast/api/blast_rps_options.hpp Source File

m_Opts->SetRemoteProgramAndService_Blast3(

,

);

SetLookupTableDefaults();

SetQueryOptionDefaults();

SetInitialWordOptionsDefaults();

SetGappedExtensionDefaults();

SetScoringOptionsDefaults();

SetHitSavingOptionsDefaults();

SetEffectiveLengthsOptionsDefaults();

SetSubjectSequenceOptionsDefaults();

#define NCBI_XBLAST_EXPORT

NULL operations for other cases.

Declares the CBlastProteinOptionsHandle class.

Handle to the options to the BLAST algorithm.

EAPILocality

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

@ eLocal

To be used for running BLAST locally.

Handle to the rpsblast options to the BLAST algorithm.

@ eCompositionBasedStats

Composition-based statistics as in NAR 29:2994-3005, 2001.

@ eNoCompositionBasedStats

Don't use composition based statistics.

bool GetSegFiltering() const

Is SEG filtering enabled?

void SetSegFilteringHicut(double hicut)

Set hicut parameter for seg.

double GetSegFilteringHicut() const

Get hicut parameter for seg.

double GetSegFilteringLocut() const

Get locut parameter for seg.

void SetCompositionBasedStats(bool mode)

Set composition based statistics mode.

double GetXDropoff() const

Returns XDropoff.

void SetSegFilteringLocut(double locut)

Set locut parameter for seg.

virtual void SetRemoteProgramAndService_Blast3()

Set the program and service name for remote blast.

int GetGapExtensionCost() const

Returns GapExtensionCost.

bool GetCompositionBasedStats(void) const

Get composition based statistics mode.

void SetSegFilteringWindow(int window)

Set window parameter for seg.

CBlastRPSOptionsHandle(const CBlastRPSOptionsHandle &rhs)

Disallow copy constructor.

int GetGapOpeningCost() const

Returns GapOpeningCost.

int GetWordSize() const

Returns WordSize.

double GetWordThreshold() const

Returns WordThreshold.

CBlastRPSOptionsHandle & operator=(const CBlastRPSOptionsHandle &rhs)

Disallow assignment operator.

int GetSegFilteringWindow() const

Get window parameter for seg.

void SetSegFiltering(bool val)

Enable SEG filtering.

void SetXDropoff(double x)

Sets XDropoff.

#define END_NCBI_SCOPE

End previously defined NCBI scope.

#define END_SCOPE(ns)

End the previously defined scope.

#define BEGIN_NCBI_SCOPE

Define ncbi namespace.

#define BEGIN_SCOPE(ns)

Define a new scope.

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