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

CUniformSearchTest;

CBlastTabularFormatThread;

EAPILocality GetLocality()

;

Validate()

;

IsIterativeSearch()

;

GetWordThreshold()

;

SetWordThreshold(

w);

GetWordSize()

;

SetWordSize(

ws);

GetLookupTableStride()

;

SetLookupTableStride(

);

GetLookupDbFilter(

)

;

SetLookupDbFilter(

);

GetMaxDbWordCount(

)

;

SetMaxDbWordCount(

num);

GetMBTemplateLength()

;

SetMBTemplateLength(

);

GetMBTemplateType()

;

SetMBTemplateType(

);

ClearFilterOptions();

GetMaskAtHash()

;

SetMaskAtHash(

=

);

GetDustFiltering()

;

SetDustFiltering(

=

);

GetDustFilteringLevel()

;

SetDustFilteringLevel(

m);

GetDustFilteringWindow()

;

SetDustFilteringWindow(

m);

GetDustFilteringLinker()

;

SetDustFilteringLinker(

m);

GetSegFiltering()

;

SetSegFiltering(

=

);

GetSegFilteringWindow()

;

SetSegFilteringWindow(

m);

GetSegFilteringLocut()

;

SetSegFilteringLocut(

m);

GetSegFilteringHicut()

;

SetSegFilteringHicut(

m);

GetRepeatFiltering()

;

SetRepeatFiltering(

=

);

* GetRepeatFilteringDB()

;

SetRepeatFilteringDB(

* db);

GetWindowMaskerTaxId()

;

SetWindowMaskerTaxId(

taxid);

* GetWindowMaskerDatabase()

;

SetWindowMaskerDatabase(

* db);

GetReadQualityFiltering()

;

SetReadQualityFiltering(

=

);

GetReadMaxFractionAmbiguous()

;

SetReadMaxFractionAmbiguous(

);

GetReadMinDimerEntropy()

;

SetReadMinDimerEntropy(

);

GetQueryGeneticCode()

;

SetQueryGeneticCode(

gc);

GetWindowSize()

;

SetWindowSize(

w);

GetOffDiagonalRange()

;

SetOffDiagonalRange(

);

GetXDropoff()

;

SetXDropoff(

x);

GetGapXDropoff()

;

SetGapXDropoff(

x);

GetGapXDropoffFinal()

;

SetGapXDropoffFinal(

x);

GetGapTrigger()

;

SetGapTrigger(

);

GetSmithWatermanMode()

;

SetSmithWatermanMode(

m =

);

GetUnifiedP()

;

SetUnifiedP(

u = 0);

GetMaxMismatches()

;

SetMaxMismatches(

m);

GetMismatchWindow()

;

SetMismatchWindow(

w);

GetChaining()

;

SetChaining(

ch);

GetHitlistSize()

;

SetHitlistSize(

s);

GetMaxNumHspPerSequence()

;

SetMaxNumHspPerSequence(

m);

GetMaxHspsPerSubject()

;

SetMaxHspsPerSubject(

m);

GetCullingLimit()

;

SetCullingLimit(

s);

GetSubjectBestHit()

;

SetSubjectBestHit();

GetBestHitOverhang()

;

SetBestHitOverhang(

overhang);

GetBestHitScoreEdge()

;

SetBestHitScoreEdge(

score_edge);

GetEvalueThreshold()

;

SetEvalueThreshold(

eval);

SetCutoffScore(

s);

vector<double> GetCutoffScoreCoeffs()

;

SetCutoffScoreCoeffs(

vector<double>& c);

GetPercentIdentity()

;

SetPercentIdentity(

p);

GetMaxEditDistance()

;

SetMaxEditDistance(

e);

GetQueryCovHspPerc()

;

SetQueryCovHspPerc(

p);

GetMinDiagSeparation()

;

SetMinDiagSeparation(

d);

GetSumStatisticsMode()

;

SetSumStatisticsMode(

m =

);

GetLongestIntronLength()

;

SetLongestIntronLength(

);

GetGappedMode()

;

SetGappedMode(

m =

);

GetMaskLevel()

;

SetMaskLevel(

s);

GetComplexityAdjMode()

;

SetComplexityAdjMode(

m =

);

GetLowScorePerc()

;

SetLowScorePerc(

p = 0.0);

GetPaired()

;

SetPaired(

p);

GetSpliceAlignments()

;

SetSpliceAlignments(

s);

* GetMatrixName()

;

SetMatrixName(

* matrix);

GetMatchReward()

;

SetMatchReward(

);

GetMismatchPenalty()

;

SetMismatchPenalty(

p);

GetGapOpeningCost()

;

SetGapOpeningCost(

);

GetGapExtensionCost()

;

SetGapExtensionCost(

e);

GetFrameShiftPenalty()

;

SetFrameShiftPenalty(

p);

GetOutOfFrameMode()

;

SetOutOfFrameMode(

m =

);

GetDbLength()

;

SetDbLength(

);

GetDbSeqNum()

;

SetDbSeqNum(

);

GetEffectiveSearchSpace()

;

SetEffectiveSearchSpace(

eff);

SetEffectiveSearchSpace(

vector<Int8>& eff);

GetDbGeneticCode()

;

SetDbGeneticCode(

gc);

* GetPHIPattern()

;

SetPHIPattern(

* pattern,

is_dna);

GetInclusionThreshold()

;

SetInclusionThreshold(

u);

GetPseudoCount()

;

SetPseudoCount(

u);

GetIgnoreMsaMaster()

;

SetIgnoreMsaMaster(

);

GetDomainInclusionThreshold(

)

;

SetDomainInclusionThreshold(

);

GetUseIndex()

;

GetForceIndex()

;

GetIsOldStyleMBIndex()

;

GetMBIndexLoaded()

;

GetIndexName()

;

SetMBIndexLoaded(

index_loaded =

);

use_index =

,

& index_name =

,

force_index =

,

old_style_index =

);

DoneDefaults()

;

SetDefaultsMode(

dmode);

GetDefaultsMode()

;

x_Throwx(

&

)

;

CDbBlast;

CDbBlastTraceback;

CDbBlastPrelim;

class ::CBlastTabularFormatThread;

class ::CTracebackTestFixture;

class ::CBlastSetupTestFixture;

class ::CUniformSearchTest;

class ::CTracebackSearchTestFixture;

User-defined methods of the data storage class.

Contains C++ wrapper classes to structures in algo/blast/core as well as some auxiliary functions to ...

@ eBoth

Both preliminary and traceback stages.

Declares the BLAST exception class.

#define NCBI_XBLAST_EXPORT

NULL operations for other cases.

The structures and functions in blast_options.

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.

EBlastProgramType

Defines the engine's notion of the different applications of the BLAST algorithm.

Definitions of special type used in BLAST.

EProgram

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

Initializes and uninitializes the genetic code singleton as if it was an automatic variable (to facil...

Runs the BLAST algorithm between 2 sequences.

Encapsulates all blast input parameters.

Class that allows the transfer of data structures from the CBlastOptionsLocal class to either the BLA...

Encapsulates all blast input parameters.

Encapsulates ALL the BLAST algorithm's options.

ncbi::objects::CBlast4_parameters TBlast4Opts

This returns a list of parameters for remote searches.

CBlastOptionsLocal * m_Local

bool m_DefaultsMode

Defaults mode (remote options will ignore Set ops).

CBlastOptions & operator=(const CBlastOptions &bo)

Prohibit assignment operator.

CAutomaticGenCodeSingleton m_GenCodeSingletonVar

This field is add.

void SetRemoteProgramAndService_Blast3(const string &p, const string &s)

Set the program and service name for remote blast.

EAPILocality

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

@ eLocal

To be used for running BLAST locally.

@ eRemote

To be used when running BLAST remotely.

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

Get the program and service name for remote blast.

CBlastOptions(const CBlastOptions &bo)

Prohibit copy c-tor.

string m_ServiceName

Service Name for Blast3.

string m_ProgramName

Program Name for Blast3.

CBlastOptionsRemote * m_Remote

Memento class to save, replace out, and restore the effective search space options of the CBlastOptio...

Constants used in compositional score matrix adjustment.

ECompoAdjustModes

An collection of constants that specify all permissible modes of composition adjustment.

static unsigned char depth[2 *(256+1+29)+1]

bool operator==(const CEquivRange &A, const CEquivRange &B)

virtual void DebugDump(CDebugDumpContext ddc, unsigned int depth) const

Define method for dumping debug information.

uint8_t Uint1

1-byte (8-bit) unsigned integer

uint32_t Uint4

4-byte (32-bit) unsigned integer

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.

bool operator!=(const CNCBI_IPAddr &lhs, unsigned int rhs)

ENa_strand

strand of nucleic acid

<!DOCTYPE HTML >< html > n< header > n< title > PubSeq Gateway Help Page</title > n< style > n th

Int4 GetCutoffScore(Int4 query_length)

Get alignment cutoff score for a given query length.

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

static SLJIT_INLINE sljit_ins l(sljit_gpr r, sljit_s32 d, sljit_gpr x, sljit_gpr b)

static SLJIT_INLINE sljit_ins msg(sljit_gpr r, sljit_s32 d, sljit_gpr x, sljit_gpr b)

Options used to create the ReadDBFILE structure Include database name and various information for res...

Options for setting up effective lengths and search spaces.

Options used for gapped extension These include: a.

Options used when evaluating and saving hits These include: a.

Options needed for initial word finding and processing.

Scoring options block Used to produce the BlastScoreBlk structure This structure may be needed for lo...

Options needed to construct a lookup table Also needed: query sequence and query length.

Options used in protein BLAST only (PSI, PHI, RPS and translated BLAST) Some of these possibly should...

Options required for setting up the query sequence.

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

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