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Showing content from http://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/doxyhtml/build__alnvec__job_8cpp_source.html below:

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

: m_Descr(

),

m_SelectAnchor(select_anchor)

err_msg, logMsg =

;

( aex.GetErrCode() ){

err_msg =

;

err_msg =

+ aex.GetMsg();

err_msg = logMsg +

() +

+aex.GetMsg();

}

(std::exception& e) {

(!err_msg.empty()) {

(n_align == 1 &&

[0]->GetSegs().IsDenseg()) {

=

;

anchor_index = -1;

(

= 0;

< n_align;

++) {

check_anchor = check_anchor && aln.CheckNumRows() == 2;

ids[0] =

(&aln.GetSeq_id(0));

ids[1] =

(&aln.GetSeq_id(1));

}

(anchor_index == -1) {

(ids[0]->Match(aln.GetSeq_id(0))) {

(ids[1]->Match(aln.GetSeq_id(1))) {

anchor_index = (anchor_index == 0) ? -1 : 1;

}

(ids[anchor_index]->Match(aln.GetSeq_id(anchor_index)) ==

) {

check_anchor =

;

(check_anchor && anchor_index != -1)

(anchor_id, ids[anchor_index]);

(

= 0;

< row_num; ++

) {

(anchor_row == -1) {

}

(std::exception&) {

(

);

(

= 0;

< row_num; ++

) {

}

(std::exception&) {

(anchor_row != -1)

static CRef< CScope > m_Scope

USING_SCOPE(ncbi::objects)

TSegTypeFlags GetSegType(TNumrow row, TNumseg seg, int offset=0) const

const CSeq_id & GetSeqId(TNumrow row) const

TDim GetNumRows(void) const

void Add(const CDense_seg &ds, TAddFlags flags=0)

void Merge(TMergeFlags flags=0)

const CDense_seg & GetDenseg(void) const

CScope & GetScope(void) const

const CBioseq_Handle & GetBioseqHandle(TNumrow row) const

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

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

virtual CRef< CObject > GetResult()

Returns the Job Result.

vector< CConstRef< objects::CSeq_align > > TAligns

CBuildAlnVecJob(const TAligns &aligns, objects::CScope &scope, bool select_anchor=false)

CBuildAlnVecJob.

CRef< CBuildAlnVecResult > m_Result

virtual ~CBuildAlnVecJob()

virtual CConstIRef< IAppJobProgress > GetProgress()

return progress object, the function shall be synchronized internally.

virtual void SetTaskCompleted(int completed)

virtual void SetTaskTotal(int total)

virtual CConstIRef< IAppJobError > GetError()

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

virtual string GetDescr() const

Returns a human readable description of the Job (optional)

CRef< objects::CScope > m_Scope

virtual bool InterruptTask()

virtual void SetTaskName(const string &name)

virtual EJobState Run()

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

CRef< CAppJobError > m_Error

CRef< objects::CAlnVec > m_AlnVec

void SetTaskProgressCallback(ITaskProgressCallback *callback)

Hook a callback to a task.

void swap(NCBI_NS_NCBI::pair_base_member< T1, T2 > &pair1, NCBI_NS_NCBI::pair_base_member< T1, T2 > &pair2)

#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)

const string & GetMsg(void) const

Get message string.

void Warning(CExceptionArgs_Base &args)

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)

bool Match(const CSeq_id &sid2) const

Match() - TRUE if SeqIds are equivalent.

CConstRef< C > ConstRef(const C *object)

Template function for conversion of const object pointer to CConstRef.

TObjectType * GetPointer(void) THROWS_NONE

Get pointer,.

void Reset(void)

Reset reference object.

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.

unsigned int

A callback function used to compare two keys in a database.

#define row(bind, expected)

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