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

:

(

), m_Params(params)

path,

, ext;

(bam_index.empty()) {

bam_index = path +

+

;

(!

(bam_index).Exists()) {

bam_index = path +

+

;

= graph->GetLoc().GetId();

writer.

(new_annot ? *new_annot : *seq_annot);

err_msg =

;

(err_msg.empty()) {

User-defined methods of the data storage class.

User-defined methods of the data storage class.

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

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

static CRef< objects::CSeq_annot > CreateCoverageGraphs(const string &bam_file, const string &index_file, const string &annot_name, const string &assembly, int bin_size=1000, TSeqIdsVector *ids=0, bool is_esitmated=false, ICanceled *canceled=0)

static bool GetCoverageGraphInfo(const objects::CSeq_annot &seq_annot, string &bam_data, string &bam_index, string &assembly)

vector< CConstRef< objects::CSeq_id > > TSeqIdsVector

void SetCanceler(ICanceled *pCanceller)

CWiggleExportParams m_Params

CRef< objects::CSeq_annot > x_RecalculateGraph(const objects::CSeq_annot &seq_annot, objects::CScope &scope)

virtual EJobState Run()

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

CWiggleExportJob(const CWiggleExportParams &params)

wxString GetFileName() const

const TConstScopedObjects & GetObjects()

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

Write a raw Seq-annot to the internal output stream.

bool WriteFooter() override

Write a file trailer.

std::ofstream out("events_result.xml")

main entry point for tests

#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)

static void SplitPath(const string &path, string *dir=0, string *base=0, string *ext=0)

Split a path string into its basic components.

ICanceled * x_GetICanceled()

CRef< CAppJobError > m_Error

string m_Descr

mutex to sync our internals

EJobState

Job states (describe FSM)

virtual void x_SetStatusText(const string &text)

vector< SConstScopedObject > TConstScopedObjects

CConstRef< C > ConstRef(const C *object)

Template function for conversion of const object pointer to CConstRef.

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.

const TGraph & GetGraph(void) const

Get the variant data.

const TData & GetData(void) const

Get the Data member data.

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

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