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NCBI C++ ToolKit: src/algo/blast/api/blast_options_cxx.cpp Source File

: m_DefaultsMode(

)

m_ReqOpts.Reset(

objects::CBlast4_parameters);

: m_DefaultsMode(

)

x_DoDeepCopy(optsRemote);

x_DoDeepCopy(optsRemote);

x2 = x; SetValue(opt, x2);

x2 = x; SetValue(opt, x2);

x2 = x; SetValue(opt, x2);

x2 = x; SetValue(opt, x2);

m_DefaultsMode = dmode;

m_DefaultsMode;

(&optsRemote !=

)

m_ReqOpts.

(

objects::CBlast4_parameters);

m_ReqOpts->Assign(*optsRemote.

);

x_SetOneParam(name, &

);

v->SetString().assign((x && (*x)) ? (*x) :

);

v->SetBig_integer(*x);

v->SetStrand_type(*x);

objects::CBlast4_parameter TParam;

((**iter).GetName() == p->GetName()) {

m_ReqOpts->Set().push_back(p);

list< CRef<objects::CBlast4_parameter> > TParamList;

TParamList::iterator TParamIter;

& nm =

.GetName();

TParamList & lst = m_ReqOpts->Set();

TParamIter pos = lst.begin(), end = lst.end();

TParamIter current = pos;

((**current).GetName() == nm) {

m_DefaultsMode(

)

(locality !=

) {

sprintf(errbuf,

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set_strand =

;

objects::CBlast4_cutoff TCutoff;

cutoff->SetRaw_score(v);

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objects::CBlast4_cutoff TCutoff;

cutoff->SetE_value(v);

objects::CBlast4_cutoff TCutoff;

cutoff->SetE_value(v);

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use_index,

& index_name,

force_index,

old_style_index )

use_index, index_name, force_index, old_style_index );

( !index_name.empty() ) {

(

);

User-defined methods of the data storage class.

User-defined methods of the data storage class.

User-defined methods of the data storage class.

#define NCBI_XBLAST_EXPORT

NULL operations for other cases.

Ungapped extension structures that are common to nucleotide and protein extension routines.

Classes that capture the state of the BLAST options (or subsets of options) and restore them later (u...

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 class to encapsulate all BLAST options.

Private header for local representation of BLAST options.

ESeedContainerType

specifies the data structures used for bookkeeping during computation of ungapped extensions

Boolean Blast_QueryIsTranslated(EBlastProgramType p)

Returns true if the query is translated.

Boolean Blast_QueryIsNucleotide(EBlastProgramType p)

Returns true if the query is nucleotide.

Boolean Blast_QueryIsProtein(EBlastProgramType p)

Returns true if the query is protein.

EBlastProgramType

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

Internal auxiliary setup classes/functions for C++ BLAST APIs.

EProgram

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

@ eDeltaBlast

Delta Blast.

@ ePSITblastn

PSI Tblastn.

Field properties for options in a Blast4 parameter list.

static const string & GetName(EBlastOptIdx opt)

static CBlast4Field & Get(EBlastOptIdx opt)

Defines BLAST error codes (user errors included)

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).

CAutomaticGenCodeSingleton m_GenCodeSingletonVar

This field is add.

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.

string m_ServiceName

Service Name for Blast3.

string m_ProgramName

Program Name for Blast3.

CBlastOptionsRemote * m_Remote

ECompoAdjustModes

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

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

void SetMinDiagSeparation(int d)

vector< double > GetCutoffScoreCoeffs() const

void SetPHIPattern(const char *pattern, bool is_dna)

BlastHitSavingOptions * GetHitSaveOpts() const

Returns BlastHitSavingOptions for eLocal objects, NULL for eRemote.

void SetMBTemplateType(unsigned char type)

double GetGapXDropoff() const

int GetMaxMismatches() const

CBlastOptions(EAPILocality locality=eLocal)

Constructor which allows specification of local or remote version of the options (might change in the...

int GetDbGeneticCode() const

void SetValue(EBlastOptIdx opt, const unsigned char &x)

void SetDustFilteringWindow(int m)

double GetSegFilteringLocut() const

void SetInclusionThreshold(double u)

void SetCompositionBasedStats(ECompoAdjustModes mode)

void DebugDump(CDebugDumpContext ddc, unsigned int depth) const

Allows to dump a snapshot of the object.

double GetBestHitOverhang() const

void SetReadMinDimerEntropy(int val)

void x_SetOneParam(CBlast4Field &field, const Int8 *x)

BlastScoringOptions * GetScoringOpts() const

void SetPHIPattern(const char *pattern, bool is_dna)

int GetWindowMaskerTaxId() const

Returns the tax id used for the windowmasker database to use, if set via SetWindowMaskerTaxId (otherw...

LookupTableOptions * GetLutOpts() const

Returns LookupTableOptions for eLocal objects, NULL for eRemote.

void SetMaxDbWordCount(Uint1 val)

BlastExtensionOptions * GetExtnOpts() const

void SetHitlistSize(int s)

void SetMismatchPenalty(int p)

int GetMaxHspsPerSubject() const

void SetStrandOption(objects::ENa_strand s)

void x_Throwx(const string &msg) const

void SetOutOfFrameMode(bool m=true)

void SetLookupDbFilter(bool val)

double GetInclusionThreshold() const

CRef< objects::CBlast4_parameters > m_ReqOpts

void SetPseudoCount(int u)

double GetPercentIdentity() const

void SetWindowSize(int w)

bool GetReadQualityFiltering(void) const

double GetEvalueThreshold() const

void SetDustFilteringLinker(int m)

Uint4 GetLookupTableStride() const

Skip words after each collected one while creating a lookup table (currently only for megablast)

double GetLowScorePerc() const

Sets low score percentages.

int GetDustFilteringLevel() const

void ClearFilterOptions()

unsigned char GetMBTemplateType() const

double GetSegFilteringLocut() const

void SetCutoffScore(int s)

unsigned char GetMBTemplateType() const

const CBlastOptionsMemento * CreateSnapshot() const

Create a snapshot of the state of this object for internal use of its data structures (BLAST C++ APIs...

void SetUnifiedP(int u=0)

void SetGapExtnAlgorithm(EBlastPrelimGapExt a)

EBlastPrelimGapExt GetGapExtnAlgorithm() const

EAPILocality GetLocality() const

Return the locality used when the object was created.

EProgram GetProgram() const

Accessors/Mutators for individual options.

void SetEvalueThreshold(double eval)

void SetWindowSize(int w)

void SetWindowMaskerTaxId(int taxid)

Sets the tax id to select an appropriate windowmasker database Conversion algorithm from tax id to da...

ECompoAdjustModes GetCompositionBasedStats() const

int GetFrameShiftPenalty() const

void SetQueryCovHspPerc(double p)

void SetSegFilteringLocut(double m)

bool GetMBIndexLoaded() const

const char * GetPHIPattern() const

void SetOutOfFrameMode(bool m=true)

const char * GetMatrixName() const

void SetReadMaxFractionAmbiguous(double val)

Set maximum fraction of ambiguous bases for next-generation read quality filtering.

void SetRepeatFiltering(bool val=true)

void SetDomainInclusionThreshold(double th)

void SetValue(EBlastOptIdx opt, const EProgram &x)

PSIBlastOptions * GetPSIBlastOpts() const

void SetDustFilteringLinker(int m)

bool operator==(const CBlastOptions &rhs) const

BlastHitSavingOptions * GetHitSaveOpts() const

BlastExtensionOptions * GetExtnOpts() const

Returns BlastExtensionOptions for eLocal objects, NULL for eRemote.

double GetEvalueThreshold() const

int GetMaxEditDistance() const

const string GetIndexName() const

Uint1 GetMaxDbWordCount(void) const

void SetEvalueThreshold(double eval)

int GetWindowMaskerTaxId() const

CBlastOptionsRemote(void)

const char * GetPHIPattern() const

void SetSegFilteringHicut(double m)

void SetGapOpeningCost(int g)

BlastInitialWordOptions * GetInitWordOpts() const

Returns BlastInitialWordOptions for eLocal objects, NULL for eRemote.

EBlastTbackExt GetGapTracebackAlgorithm() const

void SetHitlistSize(int s)

void SetQueryGeneticCode(int gc)

double GetDomainInclusionThreshold(void) const

void SetMatchReward(int r)

void SetDustFiltering(bool val=true)

double GetBestHitOverhang() const

ELookupTableType GetLookupTableType() const

objects::ENa_strand GetStrandOption() const

int GetPseudoCount() const

void SetReadMaxFractionAmbiguous(double val)

void x_SetOneParam(CBlast4Field &field, const int *x)

int GetMatchReward() const

void SetEffectiveSearchSpace(Int8 eff)

int GetMinDiagSeparation() const

bool GetSubjectBestHit() const

int GetMinDiagSeparation() const

void SetComplexityAdjMode(bool m=true)

int GetGapExtensionCost() const

void SetGapExtensionCost(int e)

void SetPseudoCount(int ps)

void SetBestHitScoreEdge(double score_edge)

int GetOffDiagonalRange() const

vector< double > GetCutoffScoreCoeffs() const

int GetOffDiagonalRange() const

double GetDomainInclusionThreshold() const

void SetFrameShiftPenalty(int p)

void SetMaxMismatches(int m)

bool GetGappedMode() const

Returns true if gapped BLAST is set, false otherwise.

int GetMaxNumHspPerSequence() const

void SetReadQualityFiltering(bool val=true)

Turn on/off next-generation read quality filtering with deafult parameters.

void ResetValue(CBlast4Field &opt)

Remove any objects matching this Blast4 field object.

void SetRepeatFilteringDB(const char *db)

Sets the repeat filtering database to use.

int GetDustFilteringLevel() const

void SetGapTracebackAlgorithm(EBlastTbackExt a)

int GetFrameShiftPenalty() const

int GetCutoffScore() const

QuerySetUpOptions * GetQueryOpts() const

void SetWindowMaskerDatabase(const char *db)

Sets the windowmasker database to use.

void SetIgnoreMsaMaster(bool val)

int GetHitlistSize() const

int GetCutoffScore() const

void SetWordThreshold(double w)

Sets WordThreshold.

double GetQueryCovHspPerc() const

bool GetLookupDbFilter(void) const

void SetDbSeqNum(unsigned int n)

void SetRepeatFilteringDB(const char *db)

void SetMaxHspsPerSubject(int m)

int GetDbGeneticCode() const

void SetGapExtensionCost(int e)

bool GetSmithWatermanMode() const

bool GetSpliceAlignments() const

Splice HSPs for each query (for mappring RNA-Seq reads to a genome)

int GetMismatchWindow() const

void SetSumStatisticsMode(bool m=true)

void SetUnifiedP(int u=0)

void SetEffectiveSearchSpace(Int8 eff)

bool GetLookupDbFilter(void) const

Int8 GetEffectiveSearchSpace() const

void SetLowScorePerc(double p=0.0)

void SetProgram(EProgram p)

Sets the task this object is best suited for.

void SetGapExtnAlgorithm(EBlastPrelimGapExt a)

BlastDatabaseOptions * GetDbOpts() const

void SetUseIndex(bool use_index=true, const string &index_name="", bool force_index=false, bool old_style_index=false)

double GetGapTrigger() const

void SetDustFilteringWindow(int m)

bool IsIterativeSearch() const

void x_AttachValue(CRef< objects::CBlast4_parameter > p)

void SetMBIndexLoaded(bool index_loaded=true)

void SetCutoffScoreCoeffs(const vector< double > &c)

void SetIgnoreMsaMaster(bool val)

int GetGapExtensionCost() const

void SetMismatchPenalty(int p)

bool GetSumStatisticsMode() const

Sum statistics options.

void SetCutoffScoreCoeffs(const vector< double > &c)

void SetOffDiagonalRange(int r)

void SetMismatchWindow(int w)

int GetQueryGeneticCode() const

void SetOffDiagonalRange(int r)

void SetReadQualityFiltering(bool val=true)

void SetGapXDropoffFinal(double x)

void SetValue(EBlastOptIdx opt, const short &x)

void SetQueryGeneticCode(int gc)

void SetMatrixName(const char *matrix)

bool GetComplexityAdjMode() const

Returns true if cross_match-like complexity adjusted.

BlastEffectiveLengthsOptions * GetEffLenOpts() const

Returns BlastEffectiveLengthsOptions for eLocal objects, NULL for eRemote.

void SetMaskAtHash(bool val=true)

void SetUseIndex(bool use_index=true, const string &index_name="", bool force_index=false, bool old_style_index=false)

void SetValue(EBlastOptIdx opt, const unsigned int &x)

double GetXDropoff() const

const string GetIndexName() const

EBlastProgramType GetProgramType() const

Returns the CORE BLAST notion of program type.

void x_Throwx(const string &msg) const

Auxiliary to throw CBlastExceptions.

int GetLongestIntronLength() const

double GetSegFilteringHicut() const

bool GetDefaultsMode() const

int GetHitlistSize() const

int GetPseudoCount() const

void SetLowScorePerc(double p=0.0)

BlastInitialWordOptions * GetInitWordOpts() const

bool Validate() const

Validate the options.

bool GetMaskAtHash() const

bool GetDustFiltering() const

void SetGapOpeningCost(int g)

void SetMBTemplateLength(unsigned char len)

bool GetRepeatFiltering() const

void SetMaxEditDistance(int e)

int GetLongestIntronLength() const

for linking HSPs with uneven gaps

void SetBestHitOverhang(double overhang)

bool GetComplexityAdjMode() const

Returns true if cross_match-like complexity adjusted.

void SetLongestIntronLength(int l)

void SetSpliceAlignments(bool s)

void SetGapXDropoff(double x)

bool GetOutOfFrameMode() const

void SetSumStatisticsMode(bool m=true)

int GetMaxNumHspPerSequence() const

double GetWordThreshold() const

void SetLookupTableStride(Uint4 val)

EProgram GetProgram() const

Accessors/Mutators for individual options.

void SetPercentIdentity(double p)

bool GetMaskAtHash() const

int GetWindowSize() const

LookupTableOptions * GetLutOpts() const

CRef< CBlastOptions > Clone() const

Explicit deep copy of the Blast options object.

int GetCullingLimit() const

const char * GetWindowMaskerDatabase() const

int GetQueryGeneticCode() const

void DebugDump(CDebugDumpContext ddc, unsigned int depth) const

Allows to dump a snapshot of the object.

int GetReadMinDimerEntropy(void) const

int GetMaskLevel() const

Masklevel filtering option -RMH-.

bool GetSplice() const

Splice HSPs for each query.

void x_DoDeepCopy(const CBlastOptions &opts)

Perform a "deep copy" of Blast options.

unsigned int GetDbSeqNum() const

int GetMismatchWindow() const

void SetSegFilteringLocut(double m)

void SetProgram(EProgram p)

char * GetFilterString() const

Return the filtering string used.

void SetFilterString(const char *f, bool clear=true)

unsigned int GetDbSeqNum() const

double GetWordThreshold() const

Returns WordThreshold.

int GetDustFilteringLinker() const

double GetSegFilteringHicut() const

int GetMaxHspsPerSubject() const

BlastScoringOptions * GetScoringOpts() const

Returns BlastScoringOptions for eLocal objects, NULL for eRemote.

void SetMinDiagSeparation(int d)

void SetXDropoff(double x)

CBlastOptionsRemote & operator=(const CBlastOptionsRemote &optsRemote)

Assignment operator.

int GetMismatchPenalty() const

EBlastPrelimGapExt GetGapExtnAlgorithm() const

void SetFilterString(const char *f)

bool GetSumStatisticsMode() const

Sum statistics options.

bool operator!=(const CBlastOptions &rhs) const

void SetValue(EBlastOptIdx opt, const objects::ENa_strand &x)

void x_SetParam(CBlast4Field &name, T &value)

int GetDustFilteringWindow() const

bool Validate() const

Validate the options.

int GetMaxMismatches() const

void SetLookupTableType(ELookupTableType type)

EBlastTbackExt GetGapTracebackAlgorithm() const

bool GetForceIndex() const

void SetReadMinDimerEntropy(int val)

Set minimum dimer entropy for next-generation read quality filtering.

void SetCullingLimit(int s)

int GetGapOpeningCost() const

QuerySetUpOptions * GetQueryOpts() const

Returns QuerySetUpOptions for eLocal objects, NULL for eRemote.

int GetSegFilteringWindow() const

void SetMBTemplateType(unsigned char type)

int GetMismatchPenalty() const

double GetQueryCovHspPerc() const

double GetInclusionThreshold() const

double GetXDropoff() const

bool GetSmithWatermanMode() const

void SetSegFilteringHicut(double m)

int GetMatchReward() const

void SetGapTrigger(double g)

CBlastOptionsRemote(const CBlastOptionsRemote &optsRemote)

Copy constructor.

void SetComplexityAdjMode(bool m=true)

void SetDefaultsMode(bool dmode)

If this is true, remote options will ignore "Set" calls.

void SetDbGeneticCode(int gc)

void SetGapTracebackAlgorithm(EBlastTbackExt a)

ECompoAdjustModes GetCompositionBasedStats() const

double GetLowScorePerc() const

Sets a low score to drop ungapped alignments if hit list is full.

int GetDustFilteringLinker() const

void SetChaining(bool ch)

void x_SetOneParam(CBlast4Field &field, CRef< objects::CBlast4_cutoff > *x)

unsigned char GetMBTemplateLength() const

Megablast only lookup table options.

bool GetIsOldStyleMBIndex() const

void SetGapTrigger(double g)

void SetMBTemplateLength(unsigned char len)

char * GetFilterString() const

double GetGapTrigger() const

double GetGapXDropoffFinal() const

bool GetIgnoreMsaMaster() const

void SetWordThreshold(double w)

vector< CConstRef< objects::CSeq_loc > > TSeqLocVector

bool GetChaining(void) const

void SetXDropoff(double x)

BlastDatabaseOptions * GetDbOpts() const

Returns BlastDatabaseOptions for eLocal objects, NULL for eRemote.

void SetChaining(bool ch)

bool GetMBIndexLoaded() const

bool GetOutOfFrameMode() const

void SetSegFiltering(bool val=true)

int GetReadMinDimerEntropy() const

Get minimum dimer entropy for next-generation read quality filtering.

PSIBlastOptions * GetPSIBlastOpts() const

Returns PSIBlastOptions for eLocal objects, NULL for eRemote.

const char * GetWindowMaskerDatabase() const

Return the name of the windowmasker database to use.

void x_SetOneParam(CBlast4Field &field, const char **x)

void SetLookupDbFilter(bool val)

void SetGapXDropoffFinal(double x)

ELookupTableType GetLookupTableType() const

unsigned char GetMBTemplateLength() const

Megablast only lookup table options.

double GetGapXDropoffFinal() const

void SetDustFilteringLevel(int m)

void SetMaskAtHash(bool val=true)

objects::ENa_strand GetStrandOption() const

double GetGapXDropoff() const

bool GetDustFiltering() const

~CBlastOptions()

Destructor.

void x_SetOneParam(CBlast4Field &field, objects::EBlast4_strand_type *x)

bool GetRepeatFiltering() const

Returns true if repeat filtering is on.

void SetBestHitScoreEdge(double score_edge)

bool GetSegFiltering() const

void SetDefaultsMode(bool dmode)

void SetDustFilteringLevel(int m)

bool GetSegFiltering() const

int GetGapOpeningCost() const

void SetDustFiltering(bool val=true)

void SetSegFiltering(bool val=true)

void SetSegFilteringWindow(int m)

bool GetReadQualityFiltering() const

Returns true if next-generation read quality filtering is turned on.

ncbi::objects::CBlast4_parameters TBlast4Opts

void x_SetOneParam(CBlast4Field &field, const bool *x)

void x_SetOneParam(CBlast4Field &field, const double *x)

int GetWindowSize() const

void SetDbGeneticCode(int gc)

void SetSegFilteringWindow(int m)

void SetGappedMode(bool m=true)

void SetCompositionBasedStats(ECompoAdjustModes mode)

void SetQueryCovHspPerc(double p)

int GetCullingLimit() const

TBlast4Opts * GetBlast4AlgoOpts()

void SetMBIndexLoaded(bool index_loaded=true)

void SetCutoffScore(int s)

void SetMaxMismatches(int m)

bool GetIgnoreMsaMaster() const

void SetPercentIdentity(double p)

const char * GetRepeatFilteringDB() const

const char * GetRepeatFilteringDB() const

Returns the name of the repeat filtering database to use.

void SetWindowMaskerTaxId(int taxid)

int GetSegFilteringWindow() const

double GetBestHitScoreEdge() const

void SetSmithWatermanMode(bool m=true)

void SetGapXDropoff(double x)

void SetMaxDbWordCount(Uint1 num)

Set maximum word count for lookup table word masking by database frequency.

void SetBestHitOverhang(double s)

void SetGappedMode(bool m=true)

Int8 GetEffectiveSearchSpace() const

TBlast4Opts * GetBlast4AlgoOpts()

void SetFrameShiftPenalty(int p)

void DoneDefaults() const

const char * GetMatrixName() const

double GetBestHitScoreEdge() const

EBlastProgramType GetProgramType() const

int GetDustFilteringWindow() const

void AddGeneticCode(int genetic_code)

Add the genetic code to the genetic code singleton.

void SetLongestIntronLength(int l)

for linking HSPs with uneven gaps

int GetMaskLevel() const

Masklevel filtering option -RMH-.

bool GetIsOldStyleMBIndex() const

double GetReadMaxFractionAmbiguous() const

Get maximum fraction of ambiguous bases for next-generation read quality filtering.

void SetMaxNumHspPerSequence(int m)

void SetMaxEditDistance(int e)

void x_ResetValue(CBlast4Field &f)

Remove values for a given Blast4 field.

void SetDomainInclusionThreshold(double incthr)

int GetMaxEditDistance() const

void SetDbSeqNum(unsigned int n)

bool GetForceIndex() const

void SetLookupTableStride(Uint4 val)

double GetPercentIdentity() const

void SetMaxHspsPerSubject(int m)

void SetSmithWatermanMode(bool m=true)

void SetInclusionThreshold(double incthr)

void SetStrandOption(objects::ENa_strand s)

void SetMismatchWindow(int w)

void SetCullingLimit(int s)

bool GetSubjectBestHit() const

Uint1 GetMaxDbWordCount(void) const

Get maximum word count for lookup table word masking by database frequency.

void SetLookupTableType(ELookupTableType type)

void SetWindowMaskerDatabase(const char *db)

Uint4 GetLookupTableStride() const

void SetRepeatFiltering(bool val=true)

Turns on repeat filtering using the default repeat database, namely kDefaultRepeatFilterDb.

bool GetGappedMode() const

Returns true if gapped BLAST is set, false otherwise.

void SetMatrixName(const char *matrix)

void SetMaxNumHspPerSequence(int m)

double GetReadMaxFractionAmbiguous(void) const

void x_DoDeepCopy(const CBlastOptionsRemote &optsRemote)

Perform a "deep copy" of remote Blast options.

void SetMatchReward(int r)

BlastEffectiveLengthsOptions * GetEffLenOpts() const

#define NON_CONST_ITERATE(Type, Var, Cont)

Non constant version of ITERATE macro.

#define NCBI_THROW(exception_class, err_code, message)

Generic macro to throw an exception, given the exception class, error code and message string.

void Reset(void)

Reset reference object.

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 USING_SCOPE(ns)

Use the specified namespace.

#define END_SCOPE(ns)

End the previously defined scope.

#define BEGIN_NCBI_SCOPE

Define ncbi namespace.

#define BEGIN_SCOPE(ns)

Define a new scope.

static int CompareNocase(const CTempString s1, SIZE_TYPE pos, SIZE_TYPE n, const char *s2)

Case-insensitive compare of a substring with another string.

EBlast4_strand_type

Access to EBlast4_strand_type's attributes (values, names) as defined in spec.

@ eBlast4_strand_type_reverse_strand

@ eBlast4_strand_type_forward_strand

@ eBlast4_strand_type_both_strands

ENa_strand

strand of nucleic acid

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

Names used in blast4 network communications.

EBlastOptIdx

Index of remote BLAST options.

@ eBlastOpt_WordThreshold

@ eBlastOpt_ComplexityAdjMode

@ eBlastOpt_MismatchPenalty

@ eBlastOpt_CompositionBasedStats

@ eBlastOpt_SubjectBestHit

@ eBlastOpt_LookupTableType

@ eBlastOpt_QueryGeneticCode

@ eBlastOpt_SegFilteringHicut

@ eBlastOpt_QueryCovHspPerc

@ eBlastOpt_GapXDropoffFinal

@ eBlastOpt_DustFilteringLevel

@ eBlastOpt_OutOfFrameMode

@ eBlastOpt_MBTemplateLength

@ eBlastOpt_BestHitOverhang

@ eBlastOpt_PercentIdentity

@ eBlastOpt_SegFilteringWindow

@ eBlastOpt_IgnoreMsaMaster

@ eBlastOpt_WindowMaskerTaxId

@ eBlastOpt_GapExtensionCost

@ eBlastOpt_GapOpeningCost

@ eBlastOpt_MaxHspsPerSubject

@ eBlastOpt_SmithWatermanMode

@ eBlastOpt_GapExtnAlgorithm

@ eBlastOpt_EvalueThreshold

@ eBlastOpt_RepeatFilteringDB

@ eBlastOpt_DomainInclusionThreshold

@ eBlastOpt_BestHitScoreEdge

@ eBlastOpt_LongestIntronLength

@ eBlastOpt_DustFilteringLinker

@ eBlastOpt_DustFiltering

@ eBlastOpt_DbGeneticCode

@ eBlastOpt_RepeatFiltering

@ eBlastOpt_SegFilteringLocut

@ eBlastOpt_MBTemplateType

@ eBlastOpt_WindowMaskerDatabase

@ eBlastOpt_EffectiveSearchSpace

@ eBlastOpt_SumStatisticsMode

@ eBlastOpt_FrameShiftPenalty

@ eBlastOpt_MaxNumHspPerSequence

@ eBlastOpt_GapTracebackAlgorithm

@ eBlastOpt_DustFilteringWindow

@ eBlastOpt_InclusionThreshold

const GenericPointer< typename T::ValueType > T2 value

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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