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NCBI C++ ToolKit: src/gui/packages/pkg_sequence/fasta_export_job.cpp Source File

:

(

), m_Params(params)

* loc =

*

(it->object.GetPointer());

&

(iter->GetObject());

(; bioseq_iter; ++bioseq_iter) {

fasta_ostr.

(*bioseq_iter);

(whole_loc.

())

fasta_ostr.

(handle, whole_loc);

fasta_ostr.

(handle, loc);

err_msg =

;

(err_msg.empty()) {

best_id_loc->

(loc);

(

&ex_loc : loc_vector) {

(ex_loc->Equals(*best_id_loc))

loc_vector.push_back(best_id_loc);

(

&ex_loc : loc_vector) {

(ex_loc->Equals(*best_id_loc))

loc_vector.push_back(best_id_loc);

CAppJobError Default implementation for IAppJobError - encapsulates a text error message.

CAppJob - default implementation of IAppJob that could be used as a base class.

CFastaExportParams m_Params

CFastaExportJob(const CFastaExportParams &params)

bool x_CheckForDuplicates(const objects::CSeq_loc &loc, TLocVector &loc_vector, objects::CScope &scope) const

virtual EJobState Run()

Function that does all the useful work, called by the Engine.

CConstRef< objects::CSeq_loc > x_GetWholeLoc(const objects::CSeq_loc &loc, TLocVector &loc_vector, objects::CScope &scope) const

std::vector< CConstRef< objects::CSeq_loc > > TLocVector

bool GetSaveMasterRecord() const

wxString GetFileName() const

const TConstScopedObjects & GetObjects() const

int GetExportType() const

FASTA-format output; see also ReadFasta in <objtools/readers/fasta.hpp>

static void Convert(objects::CScope &scope, const CObject &obj, const CTypeInfo *info, TObjList &objs, TFlags flags=eDefault)

Convert an object of potentially unknown type to a set of objects of known type.

ITypeConverter::TObjList TObjList

USING_SCOPE(ncbi::objects)

#define ITERATE(Type, Var, Cont)

ITERATE macro to sequence through container elements.

#define LOG_POST(message)

This macro is deprecated and it's strongly recomended to move in all projects (except tests) to macro...

const string & GetMsg(void) const

Get message string.

void Info(CExceptionArgs_Base &args)

CRef< CAppJobError > m_Error

string m_Descr

mutex to sync our internals

EJobState

Job states (describe FSM)

vector< SConstScopedObject > TConstScopedObjects

CConstRef< CSeq_id > GetSeqId(void) const

virtual void Assign(const CSerialObject &source, ESerialRecursionMode how=eRecursive)

Override Assign() to incorporate cache invalidation.

void SetId(CSeq_id &id)

set the 'id' field in all parts of this location

const CSeq_id * GetId(void) const

Get the id of the location return NULL if has multiple ids or no id at all.

const CSeq_id & GetId(const CSeq_loc &loc, CScope *scope)

If all CSeq_ids embedded in CSeq_loc refer to the same CBioseq, returns the first CSeq_id found,...

virtual void Write(const CSeq_entry_Handle &handle, const CSeq_loc *location=0)

Unspecified locations designate complete sequences; non-empty custom titles override the usual title ...

void SetFlag(EFlags flag)

@ eGetId_Best

return the "best" gi (uses FindBestScore(), with CSeq_id::CalculateScore() as the score function

@ fInstantiateGaps

honor specifed gap mode; on by default

@ fAssembleParts

assemble FAR delta sequences; on by dflt

CBioseq_Handle GetBioseqHandle(const CSeq_id &id)

Get bioseq handle by seq-id.

bool Empty(void) const THROWS_NONE

Check if CConstRef is empty – not pointing to any object which means having a null value.

void Reset(void)

Reset reference object.

#define END_NCBI_SCOPE

End previously defined NCBI scope.

#define BEGIN_NCBI_SCOPE

Define ncbi namespace.

IO_PREFIX::ofstream CNcbiOfstream

Portable alias for ofstream.

Defines classes: CDirEntry, CFile, CDir, CSymLink, CMemoryFile, CFileUtil, CFileLock,...

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