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

= args[

] ? &(args[

].AsOutputFile()) : &cout;

options = args[

].AsString();

( options ==

) {

( options ==

) {

skip = args[

].AsString();

& sid = **sid_itr;

& sid = **sid_itr;

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

*

<< gi_string <<

<< accn_string;

has_segset =

;

*

<< title << endl;

*

<< title << endl;

CSeq_entry * GetParentEntry(void) const

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

void x_FastaSeqIdWrite(const CBioseq &bioseq)

CDeflineGenerator::TUserFlags m_flags

CDeflineProcess(bool use_indexing, bool gpipe_mode)

virtual void SeqEntryInitialize(CRef< CSeq_entry > &se)

void ProcessInitialize(const CArgs &args)

CDeflineProcess(bool use_indexing)

void ProcessInitialize(const CArgs &args)

virtual void SeqEntryInitialize(CRef< CSeq_entry > &se)

CSeq_entry_Handle m_topseh

CRef< CSeq_entry > m_entry

unsigned int m_objectcount

CSeq_entry * GetParentEntry(void) const

API (CDeflineGenerator) for computing sequences' titles ("definitions").

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.

int TUserFlags

Binary "OR" of EUserFlags.

@ fGpipeMode

Use GPipe defaults.

@ fShowModifiers

Show key-value pair modifiers (e.g. "[organism=Homo sapiens]")

@ fIgnoreExisting

Generate fresh titles unconditionally.

IO_PREFIX::ostream CNcbiOstream

Portable alias for ostream.

static SIZE_TYPE Find(const CTempString str, const CTempString pattern, ECase use_case=eCase, EDirection direction=eForwardSearch, SIZE_TYPE occurrence=0)

Find the pattern in the string.

void Start(void)

Start the timer.

E_Choice Which(void) const

Which variant is currently selected.

E_Choice

Choice variants.

bool IsSetClass(void) const

Check if a value has been assigned to Class data member.

TClass GetClass(void) const

Get the Class member data.

const TSet & GetSet(void) const

Get the variant data.

bool IsSet(void) const

Check if variant Set is selected.

@ eClass_parts

parts for 2 or 3

@ eClass_segset

segmented sequence + parts

TRepr GetRepr(void) const

Get the Repr member data.

ERepr

representation class

const TInst & GetInst(void) const

Get the Inst member data.

bool IsSetRepr(void) const

Check if a value has been assigned to Repr data member.

bool IsSetMol(void) const

Check if a value has been assigned to Mol data member.

bool IsSetInst(void) const

the sequence data Check if a value has been assigned to Inst data member.

TMol GetMol(void) const

Get the Mol member data.

EMol

molecule class in living organism

@ eRepr_seg

segmented sequence

@ eRepr_virtual

no seq data

@ eMol_na

just a nucleic acid

#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_SEQSETS_WITHIN_SEQENTRY(Itr, Var)

VISIT_ALL_SEQSETS_WITHIN_SEQENTRY.

#define VISIT_ALL_BIOSEQS_WITHIN_SEQENTRY(Itr, Var)

VISIT_ALL_BIOSEQS_WITHIN_SEQENTRY.

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