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

SetDefaults();

m_Opts->SetLookupTableType(

);

m_Opts->SetWordSize(ws);

m_Opts->GetStrandOption();

m_Opts->SetStrandOption(strand);

m_Opts->GetWindowMaskerDatabase();

m_Opts->SetWindowMaskerDatabase(db);

(

* matrix) { m_Opts->SetMatrixName(matrix); }

SetTraditionalBlastnDefaults();

SetTraditionalMegablastDefaults();

SetVecScreenDefaults();

m_Opts->SetRemoteProgramAndService_Blast3(

,

);

SetLookupTableDefaults();

SetMBLookupTableDefaults();

SetQueryOptionDefaults();

SetInitialWordOptionsDefaults();

SetMBInitialWordOptionsDefaults();

SetGappedExtensionDefaults();

SetMBGappedExtensionDefaults();

SetScoringOptionsDefaults();

SetMBScoringOptionsDefaults();

SetHitSavingOptionsDefaults();

SetMBHitSavingOptionsDefaults();

SetEffectiveLengthsOptionsDefaults();

SetSubjectSequenceOptionsDefaults();

#define NCBI_XBLAST_EXPORT

NULL operations for other cases.

EBlastPrelimGapExt

The algorithm to be used for preliminary gapped extensions.

EBlastTbackExt

The algorithm to be used for final gapped extensions with traceback.

ELookupTableType

Types of the lookup table.

Declares the CBlastOptionsHandle and CBlastOptionsFactory classes.

Handle to the nucleotide-nucleotide options to the BLAST algorithm.

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.

int GetDustFilteringLinker() const

Get linker parameter for dust.

void SetLookupTableType(ELookupTableType type)

Sets LookupTableType.

int GetGapExtensionCost() const

Returns GapExtensionCost.

EBlastPrelimGapExt GetGapExtnAlgorithm() const

Returns GapExtnAlgorithm.

void SetDustFilteringWindow(int window)

Set window parameter for dust.

EBlastTbackExt GetGapTracebackAlgorithm() const

Returns GapTracebackAlgorithm.

bool GetDustFiltering() const

Is dust filtering enabled?

int GetWordSize() const

Returns WordSize.

void SetMatchReward(int r)

Sets MatchReward.

int GetMatchReward() const

Returns MatchReward.

void SetGapExtnAlgorithm(EBlastPrelimGapExt algo)

Sets GapExtnAlgorithm.

void SetWindowMaskerTaxId(int taxid)

Enable window masker and select a taxid (or 0 to disable).

void SetDustFilteringLinker(int linker)

Set linker parameter for dust.

const char * GetMatrixName() const

Returns MatrixName.

double GetXDropoff() const

Returns XDropoff.

int GetDustFilteringLevel() const

Get level parameter for dust.

void SetGapTracebackAlgorithm(EBlastTbackExt algo)

Sets GapTracebackAlgorithm.

const char * GetWindowMaskerDatabase() const

Get the window masker database name (or NULL if not set).

CBlastNucleotideOptionsHandle(const CBlastNucleotideOptionsHandle &rhs)

Disallow copy constructor.

virtual void SetRemoteProgramAndService_Blast3()

Set the program and service name for remote blast.

void SetMismatchPenalty(int p)

Sets MismatchPenalty.

void SetMatrixName(const char *matrix)

Sets MatrixName.

void SetRepeatFilteringDB(const char *db)

Enable repeat filtering.

void SetXDropoff(double x)

Sets XDropoff.

void SetRepeatFiltering(bool val)

Enable repeat filtering.

bool GetRepeatFiltering() const

Is repeat filtering enabled?

int GetDustFilteringWindow() const

Get window parameter for dust.

void SetGapExtensionCost(int e)

Sets GapExtensionCost.

int GetGapOpeningCost() const

Returns GapOpeningCost.

objects::ENa_strand GetStrandOption() const

Returns StrandOption.

int GetWindowMaskerTaxId() const

Get the window masker taxid (or 0 if not set).

const char * GetRepeatFilteringDB() const

Get the repeat filtering database.

ELookupTableType GetLookupTableType() const

Returns LookupTableType.

void SetWordSize(int ws)

Sets WordSize.

CBlastNucleotideOptionsHandle & operator=(const CBlastNucleotideOptionsHandle &rhs)

Disallow assignment operator.

void SetDustFiltering(bool val)

Enable dust filtering.

int GetMismatchPenalty() const

Returns MismatchPenalty.

void SetWindowMaskerDatabase(const char *db)

Enable window masker and select a database (or NULL to disable).

void SetDustFilteringLevel(int level)

Set level parameter for dust.

void SetGapOpeningCost(int g)

Sets GapOpeningCost.

void SetStrandOption(objects::ENa_strand strand)

Sets StrandOption.

#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.

ENa_strand

strand of nucleic acid

double r(size_t dimension_, const Int4 *score_, const double *prob_, double theta_)

int g(Seg_Gsm *spe, Seq_Mtf *psm, Thd_Gsm *tdg)

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