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Showing content from http://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/doxyhtml/build__sparse__aln__job_8cpp_source.html below:

NCBI C++ ToolKit: src/gui/widgets/aln_multiple/build_sparse_aln_job.cpp Source File

: m_Descr(

),

m_AnchoredAlns(aligns),

err_msg, logMsg =

;

}

(std::exception& e) {

(!err_msg.empty()) {

(

);

row_num = alignment->

();

(

= 0;

< row_num; ++

) {

}

(std::exception&) {

static CRef< CScope > m_Scope

void BuildAln(TAnchoredAlnVec &in_alns, CAnchoredAln &out_aln, const CAlnUserOptions &options, TAlnSeqIdIRef pseudo_seqid=TAlnSeqIdIRef())

Build anchored alignment from a set of alignmnets.

USING_SCOPE(ncbi::objects)

Options for different alignment manager operations.

Query-anchored alignment can be 2 or multi-dimentional.

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

CAppJobProgress Default implementation for IAppJobProgress - the class encapsulates a text message an...

CRef< CAppJobError > m_Error

CBuildSparseAlnJob(const TAnchoredAlnVector &aligns, const TOptions &options, objects::CScope &scope)

CBuildSparseAlnJob.

CRef< CBuildSparseAlnResult > m_Result

TAnchoredAlnVector m_AnchoredAlns

virtual string GetDescr() const

Returns a human readable description of the Job (optional)

virtual bool InterruptTask()

virtual void SetTaskCompleted(int completed)

CRef< objects::CScope > m_Scope

vector< CRef< CAnchoredAln > > TAnchoredAlnVector

string m_TaskName

control alignment building

virtual void SetTaskName(const string &name)

virtual ~CBuildSparseAlnJob()

virtual EJobState Run()

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

virtual CRef< CObject > GetResult()

Returns the Job Result.

virtual void SetTaskTotal(int total)

virtual CConstIRef< IAppJobProgress > GetProgress()

return progress object, the function shall be synchronized internally.

virtual CConstIRef< IAppJobError > GetError()

Returns IAppJobError object describing internal error that caused the Job to fail.

CRef< CSparseAln > m_SparseAln

TNumrow GetNumRows(void) const

Synonym of the above.

const objects::CBioseq_Handle & GetBioseqHandle(TNumrow row) const

Get bioseq handle for the row.

#define LOG_POST(message)

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

void Error(CExceptionArgs_Base &args)

#define NCBI_THROW(exception_class, err_code, message)

Generic macro to throw an exception, given the exception class, error code and message string.

const string & GetMsg(void) const

Get message string.

string ReportAll(TDiagPostFlags flags=eDPF_Exception) const

Report all exceptions.

virtual const char * what(void) const noexcept

Standard report (includes full backlog).

virtual bool IsCanceled() const override

EJobState

Job states (describe FSM)

void SetNormDone(float done)

void SetText(const string &text)

TObjectType * GetPointer(void) THROWS_NONE

Get pointer,.

void Reset(void)

Reset reference object.

#define END_NCBI_SCOPE

End previously defined NCBI scope.

#define BEGIN_NCBI_SCOPE

Define ncbi namespace.

static string IntToString(int value, TNumToStringFlags flags=0, int base=10)

Convert int to string.

#define row(bind, expected)

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