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

CreateTask(

task,

GetDocumentation(

& task_name);

Validate()

;

SetDefaults();

* GetFilterString()

;

SetFilterString(

*

,

clear =

);

m_Opts->GetGapXDropoffFinal();

m_Opts->GetMaxNumHspPerSequence();

m_Opts->GetMaxHspsPerSubject();

()

{

m_Opts->GetDbSeqNum(); }

(

num) { m_Opts->SetDbSeqNum(num); }

m_Opts->GetEffectiveSearchSpace();

m_Opts->SetEffectiveSearchSpace(eff);

#define NCBI_XBLAST_EXPORT

NULL operations for other cases.

Declares class to encapsulate all BLAST options.

EProgram

This enumeration is to evolve into a task/program specific list that specifies sets of default parame...

Creates BlastOptionsHandle objects with default values for the programs/tasks requested.

Handle to the options to the BLAST algorithm.

Encapsulates ALL the BLAST algorithm's options.

EAPILocality

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

@ eLocal

To be used for running BLAST locally.

CBlastOptions::EAPILocality EAPILocality

Convenience define.

void SetEvalueThreshold(double eval)

Sets EvalueThreshold.

Int8 GetEffectiveSearchSpace() const

Returns EffectiveSearchSpace.

virtual void SetScoringOptionsDefaults()=0

Sets ScoringOptionsDefaults.

double GetGapTrigger() const

Returns GapTrigger.

void DoneDefaults()

Returns true if this object needs default values set.

void SetQueryCovHspPerc(double p)

Sets QueryCovHspPerc.

void SetDbLength(Int8 len)

Sets DbLength.

virtual void SetLookupTableDefaults()=0

Sets LookupTableDefaults.

virtual void SetSubjectSequenceOptionsDefaults()=0

Sets SubjectSequenceOptionsDefaults.

virtual void SetGappedExtensionDefaults()=0

Sets GappedExtensionDefaults.

int GetOffDiagonalRange() const

void SetDbSeqNum(unsigned int num)

Sets DbSeqNum.

void SetGapTrigger(double g)

Sets GapTrigger.

void SetComplexityAdjMode(bool m=true)

Sets ComplexityAdjMode -RMH-.

double GetGapXDropoffFinal() const

Returns GapXDropoffFinal.

Int8 GetDbLength() const

Returns DbLength.

int GetMaskLevel() const

Returns MaskLevel -RMH-.

void SetEffectiveSearchSpace(Int8 eff)

Sets EffectiveSearchSpace.

virtual void SetQueryOptionDefaults()=0

Sets QueryOptionDefaults.

CRef< CBlastOptions > m_Opts

Data type this class controls access to.

unsigned int GetDbSeqNum() const

Returns DbSeqNum.

CBlastOptions & SetOptions()

Returns a reference to the internal options class which this object is a handle for.

bool GetGappedMode() const

Returns GappedMode.

double GetPercentIdentity() const

Returns PercentIdentity.

void SetMaxHspsPerSubject(int m)

Sets MaxHspPerSubjectQueryPair.

virtual void SetEffectiveLengthsOptionsDefaults()=0

Sets EffectiveLengthsOptionsDefaults.

void SetHitlistSize(int s)

Sets HitlistSize.

bool m_DefaultsMode

Set to true when 'remote' options should ignore setters.

int GetMinDiagSeparation() const

Returns MinDiagSeparation.

const CBlastOptions & GetOptions() const

Return the object which this object is a handle for.

void SetWindowSize(int ws)

Sets WindowSize.

int GetMaxNumHspPerSequence() const

Returns MaxNumHspPerSequence.

bool GetMaskAtHash() const

Returns whether masking should only be done for lookup table creation.

void SetMinDiagSeparation(int d)

Sets MinDiagSeparation.

virtual void SetInitialWordOptionsDefaults()=0

Sets InitialWordOptionsDefaults.

void SetGapXDropoffFinal(double x)

Sets GapXDropoffFinal.

int GetCutoffScore() const

Returns CutoffScore.

virtual void SetRemoteProgramAndService_Blast3()=0

Set the program and service name for remote blast.

double GetLowScorePerc() const

Returns low score percentage for ungapped alignments.

void SetCullingLimit(int s)

Sets Culling limit.

double GetQueryCovHspPerc() const

Returns QueryCovHspPerc.

void SetGapXDropoff(double x)

Sets GapXDropoff.

void SetMaskAtHash(bool m=true)

Sets MaskAtHash.

void SetLowScorePerc(double p)

Sets low score percentage for ungapped alignments.

double GetGapXDropoff() const

Returns GapXDropoff.

void SetMaskLevel(int ml)

Sets MaskLevel -RMH-.

virtual void SetHitSavingOptionsDefaults()=0

Sets HitSavingOptionsDefaults.

CBlastOptionsFactory()

Private c-tor.

void SetOffDiagonalRange(int r)

int GetWindowSize() const

Returns WindowSize.

int GetHitlistSize() const

Returns HitlistSize.

void SetMaxNumHspPerSequence(int m)

Sets MaxNumHspPerSequence.

void SetGappedMode(bool m=true)

Sets GappedMode.

void SetPercentIdentity(double p)

Sets PercentIdentity.

void SetCutoffScore(int s)

Sets CutoffScore.

ETaskSets

Sets of tasks for the command line BLAST binaries.

CBlastOptions::EAPILocality EAPILocality

Convenience define.

void ClearFilterOptions()

Clears the filtering options.

int GetMaxHspsPerSubject() const

Returns MaxHspsPerSubjectQueryPair.

bool GetComplexityAdjMode() const

Returns Complexity Adjustment Mode -RMH-.

double GetEvalueThreshold() const

Returns EvalueThreshold.

int GetCullingLimit() const

Returns Culling limit.

@ eProtProt

Protein-protein tasks.

@ eNuclNucl

Nucleotide-nucleotide tasks.

@ eMapping

Mapping tasks.

int64_t Int8

8-byte (64-bit) signed integer

#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.

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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