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NCBI C++ ToolKit: src/app/streamtest/process_seqvector.hpp Source File

= args[

] ? &(args[

].AsOutputFile()) : &cout;

& sid = **sid_itr;

& sid = **sid_itr;

(gi_string.empty() || accn_string.empty()) {

*

<< gi_string <<

<< accn_string;

& title =

.GenerateDefline (bsh, 0);

*

<< title << endl;

( gap_type !=

&& sv_iter.GetGapSizeForward() > 0 ) {

gap_len = sv_iter.SkipGap();

( gap_len > 0 ) {

Class for computing sequences' titles ("definitions").

void ProcessInitialize(const CArgs &args)

virtual void SeqEntryInitialize(CRef< CSeq_entry > &se)

CSeq_entry_Handle m_topseh

CRef< CSeq_entry > m_entry

@ eGT_dashes

Multiple inline dashes.

@ eGT_one_dash

A single dash, followed by a line break.

@ eGT_count

>?N or >?unk100, as appropriate.

@ eGT_letters

Multiple inline Ns or Xs as appropriate (default).

virtual void SeqEntryInitialize(CRef< CSeq_entry > &se)

void x_FsaSeqIdWrite(const CBioseq &bioseq)

void ProcessInitialize(const CArgs &args)

static const char * str(char *buf, int n)

#define ERR_POST(message)

Error posting with file, line number information but without error codes.

void Error(CExceptionArgs_Base &args)

virtual const char * what(void) const noexcept

Standard report (includes full backlog).

const string AsFastaString(void) const

virtual void WriteAsFasta(ostream &out) const

Implement serializable interface.

CBioseq_Handle GetBioseqHandle(const CSeq_id &id)

Get bioseq handle by seq-id.

CSeqVector GetSeqVector(EVectorCoding coding, ENa_strand strand=eNa_strand_plus) const

Get sequence: Iupacna or Iupacaa if use_iupac_coding is true.

@ eCoding_Iupac

Set coding to printable coding (Iupacna or Iupacaa)

IO_PREFIX::ostream CNcbiOstream

Portable alias for ostream.

void Start(void)

Start the timer.

E_Choice Which(void) const

Which variant is currently selected.

E_Choice

Choice variants.

#define FOR_EACH_SEQID_ON_BIOSEQ(Itr, Var)

FOR_EACH_SEQID_ON_BIOSEQ EDIT_EACH_SEQID_ON_BIOSEQ.

#define NCBI_SEQID(Type)

@NAME Convenience macros for NCBI objects

#define VISIT_ALL_BIOSEQS_WITHIN_SEQENTRY(Itr, Var)

VISIT_ALL_BIOSEQS_WITHIN_SEQENTRY.

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