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

:

(

), m_Params(params)

= 0;

annot->

(*seqAnnot);

* bioseq =

*

(it->object.GetPointer());

* seqLoc =

*

(it->object.GetPointer());

iter(*scope, *seqLoc, sel);

(; iter; ++iter) {

annot->

().SetFtable().push_back(feat);

* seqId =

*

(it->object.GetPointer());

err_msg =

;

(err_msg.empty()) {

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

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

bool WriteAlign(const CSeq_align &, const string &asmblyName="", const string &asmblyAccession="") override

Write a Seq-align object.

bool WriteAnnot(const CSeq_annot &annot, const string &asmblyName="", const string &asmblyAccession="") override

Write a trailer marking the end of a parsing context.

bool WriteBioseqHandle(CBioseq_Handle bsh, const string &asmblyName="", const string &asmblyAccession="") override

Write Bioseq contained in given handle Essentially, will write all features that live on the given Bi...

bool WriteSeqEntryHandle(CSeq_entry_Handle seh, const string &asmblyName="", const string &asmblyAccession="") override

Write Seq-entry contained in a given handle.

virtual EJobState Run()

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

CGtfExportJob(const CGtfExportParams &params)

CGtfExportParams m_Params

bool GetExactFlevel() const

bool GetSuppressExonNumbers() const

wxString GetFileName() const

const TConstScopedObjects & GetObjects() const

bool GetSuppressGeneFeatures() const

wxString GetFeatureDepth() const

bool WriteHeader() override

Write a file header identifying the file content as GFF version 2.

namespace ncbi::objects::

virtual bool WriteFooter()

Write a file trailer.

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

#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

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

Set object to copy of another one.

CBioseq_Handle AddBioseq(CBioseq &bioseq, TPriority pri=kPriority_Default, EExist action=eExist_Throw)

Add bioseq, return bioseq handle.

static CRef< CObjectManager > GetInstance(void)

Return the existing object manager or create one.

CSeq_entry_Handle AddTopLevelSeqEntry(CSeq_entry &top_entry, TPriority pri=kPriority_Default, EExist action=eExist_Default)

Add seq_entry, default priority is higher than for defaults or loaders Add object to the score with p...

CBioseq_Handle GetBioseqHandle(const CSeq_id &id)

Get bioseq handle by seq-id.

void AddDefaults(TPriority pri=kPriority_Default)

Add default data loaders from object manager.

SAnnotSelector & SetExactDepth(bool value=true)

SetExactDepth() specifies that annotations will be searched on the segment level specified by SetReso...

const CSeq_feat & GetOriginalFeature(void) const

Get original feature with unmapped location/product.

SAnnotSelector & SetResolveDepth(int depth)

SetResolveDepth sets the limit of subsegment resolution in searching annotations.

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.

void SetData(TData &value)

Assign a value to Data data member.

USING_SCOPE(ncbi::objects)

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

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