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NCBI C++ ToolKit: src/algo/align/ngalign/ngalign.cpp Source File

:

(&Scope), m_AllowDupes(AllowDupes), m_GenColl(GenColl)

(*ScorerIter)->ScoreAlignments(CurrResults, *

);

(*FilterIter)->FilterAlignments(CurrResults, FilterResults, *

);

AccumResults->Insert(CurrResults);

Results = AccumResults->ToSeqAlignSet();

Results = AccumResults->ToBestSeqAlignSet();

(!Results.

()) {

FastaId =

.GetSeq_id(0).AsFastaString();

(

.GetNamedScore((*FactoryIter)->GetName(),

)) {

extra.

((*FactoryIter)->GetName(), FastaId);

static CRef< CScope > m_Scope

Declares the CBl2Seq (BLAST 2 Sequences) class.

Declares the CBlastNucleotideOptionsHandle class.

Declares the CBlastOptionsHandle and CBlastOptionsFactory classes.

Definitions of special type used in BLAST.

Main argument class for BLASTN application.

list< CIRef< IAlignmentScorer > > TScorers

CRef< objects::CGC_Assembly > m_GenColl

CRef< objects::CScope > m_Scope

virtual TAlignSetRef x_Align_Impl()

void SetQuery(ISequenceSet *Set)

void SetSubject(ISequenceSet *Set)

list< CIRef< IAlignmentFactory > > TFactories

CIRef< ISequenceSet > m_Subject

CIRef< ISequenceSet > m_Query

void AddFilter(IAlignmentFilter *Filter)

void AddAligner(IAlignmentFactory *Aligner)

void AddScorer(IAlignmentScorer *Scorer)

list< CIRef< IAlignmentFilter > > TFilters

static const char * KFILTER_SCORE

Declares the CDiscNucleotideOptionsHandle class.

#define ITERATE(Type, Var, Cont)

ITERATE macro to sequence through container elements.

#define NON_CONST_ITERATE(Type, Var, Cont)

Non constant version of ITERATE macro.

CDiagContext_Extra & Print(const string &name, const string &value)

The method does not print the argument, but adds it to the string.

CDiagContext & GetDiagContext(void)

Get diag context instance.

CDiagContext_Extra Extra(void) const

Create a temporary CDiagContext_Extra object.

#define NCBI_THROW(exception_class, err_code, message)

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

bool IsNull(void) const THROWS_NONE

Check if pointer is null – same effect as Empty().

#define END_SCOPE(ns)

End the previously defined scope.

#define BEGIN_SCOPE(ns)

Define a new scope.

static bool IsSignaled(TSignalMask signals=eSignal_Any)

Check that any of specified signals is received.

list< CRef< CSeq_align > > Tdata

Main class to perform a BLAST search on the local machine.

Magic spell ;-) needed for some weird compilers... very empiric.

GenericValue< UTF8<> > Value

GenericValue with UTF8 encoding.

Setup interrupt signal handling.

Defines NCBI C++ exception handling.

void Filter(TTimeline &timeline, TServers &servers)

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