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NCBI C++ ToolKit: src/gui/widgets/seq_graphic/feature_panel_ds.cpp Source File

& obj, objects::CScope& scope,

EJobState

();

& assembly,

& tms_context);

EJobState

();

, m_ScopedObj(&obj, &scope)

, m_DSContext(ds_context)

, m_RenderingCntx(r_cntx)

, m_ExtraParam(extra_param)

}

(

);

& assembly,

& tms_context)

, m_Assembly(assembly)

, m_TMSContext(tms_context)

vector<CRef<CAnnotMetaData> > tmsTracks;

+

+ accession +

+

+

;

(

<<

<< tmsTracks.size() <<

);

(

: tmsTracks) {

+

+ accession +

;

(annots.

(

.first) == annots.

()) {

(

<<

<<

.first);

(

&

: annots) {

(

<<

<<

.first);

}

(std::exception& e) {

.GetSeqId()->GetLabel(&id_str);

(

<<

<< id_str <<

, m_RenderingCntx(

)

, m_UseEUtils(

)

(e.GetErrCode()) {

<<

);

&

=

&

(

.object.GetObject());

sid(

);

slabel(

);

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

IAppJobListener Interface for components that need to be notified about changes in Jobs.

static CAssemblyCache & GetInstance()

virtual string GetExtensionIdentifier() const

returns the unique human-readable identifier for the extension the id should use lowercase letters se...

virtual bool IsSharable() const

check if the data source can be shared.

virtual string GetExtensionLabel() const

returns a displayable label for this extension ( please capitalize the key words - "My Extension" )

virtual ISGDataSource * CreateDS(SConstScopedObject &object) const

create an instance of the layout track type using default settings.

void SetTMSContext(const string &tms_context)

void CreateTrack(const string &desc, const ILayoutTrackFactory *factory, CTrackContainer *parent, CTempTrackProxy *params, const ILayoutTrackFactory::SExtraParams &extra_param)

CIRef< ISGDataSourceContext > m_DSContext

CRenderingContext * m_RenderingCntx

CFeaturePanelDS(objects::CScope &scope, const objects::CSeq_id &id)

TJobID m_MetaDataJob

job id for annot meta-data job id.

void GetAssemblies(const string &seqAcc)

virtual bool AllJobsFinished() const

ILayoutTrackFactory::TAnnotMetaDataList TAnnotMetaDataList

void SetUseEUtils(bool use)

void ClearMetaDataJobId()

void SetAssembly(const string &assembly)

void GetAnnotMetaData(const string &desc)

retrieve a list of annotations with their meta data.

list< CRef< objects::CGC_Assembly > > m_Assemblies

virtual EJobState Run()

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

virtual CRef< CObject > GetResult()

Returns the Job Result.

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< CAppJobError > m_Error

virtual CConstIRef< IAppJobProgress > GetProgress()

return progress object, the function shall be synchronized internally.

CGetAssembliesJob(const string &seqAcc)

CRef< CGetAssembliesJobResult > m_Result

Base class to build jobs with cancel functionality.

void Post(CRequestStatus::ECode status=CRequestStatus::e200_Ok)

CRenderingContext offers the basic context and utility methods for rendering layout objects in featur...

TJobID x_LaunchJob(IAppJob &job, int report_period=1, const string &pool="ObjManagerEngine")

Launch either a background or foreground job.

CAppJobDispatcher::TJobID TJobID

objects::CScope & GetScope(void) const

Get the scope from the handle.

virtual bool AllJobsFinished() const

void x_ForegroundJob(IAppJob &job)

objects::CBioseq_Handle m_Handle

TJobID x_BackgroundJob(IAppJob &job, int report_period, const string &pool)

Jobs on thread pool.

const string & GetCategory() const

const string & GetTrackProfile() const

const TTrackProxies & GetChildren() const

const string & GetName() const

const string & GetSource() const

const string & GetSubcategory() const

CTrackContainer - a track container in the form of layout track.

CTrackContainer * m_ParentTrack

ILayoutTrackFactory::TTrackMap m_Tracks

CRef< CTempTrackProxy > m_TrackParams

CConstIRef< ILayoutTrackFactory > m_Factory

virtual string GetDescr() const

Returns a human readable description of the Job (optional)

virtual CRef< CObject > GetResult()

Returns the Job Result.

virtual CConstIRef< IAppJobError > GetError()

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

CIRef< ISGDataSourceContext > m_DSContext

virtual EJobState Run()

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

CRef< CTrackInitJobResult > m_Result

ILayoutTrackFactory::SExtraParams m_ExtraParam

ILayoutTrackFactory::TAnnotMetaDataList TAnnotMetaDataList

virtual CConstIRef< IAppJobProgress > GetProgress()

return progress object, the function shall be synchronized internally.

virtual ~CTrackInitializationJob()

TAnnotMetaDataList m_SrcAnnots

CTrackInitializationJob(const string &desc, const ILayoutTrackFactory *factory, CTrackContainer *parent, CTempTrackProxy *params, const CObject &obj, objects::CScope &scope, ISGDataSourceContext *ds_context, CRenderingContext *r_cntx, const ILayoutTrackFactory::SExtraParams &extra_param, const TAnnotMetaDataList &src_annots)

CSeqGraphicJob implementation.

CRenderingContext * m_RenderingCntx

SConstScopedObject m_ScopedObj

CRef< CAppJobError > m_Error

ISGDSManager is seqgraphic data source manage that serves as an data source context.

const_iterator end() const

const_iterator find(const key_type &key) const

#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_CATCH(message)

Catch CExceptions as well This macro is deprecated - use *_X or *_XX variant instead of it.

void Info(CExceptionArgs_Base &args)

static bool IsNAA(const string &annot, bool isStrict=false)

check if a given annotation is a named annotation accession[.version][number] when isSctrict == false...

void GetAllNAMetaData(TNAMetaDataSet &md_set, const string &context="", ICanceled *canceledCallback=0) const

Get meta-data for a given NAA associated with seq_id.

static bool isQuasiLocal(const objects::CBioseq_Handle &handle)

check that a given accession is either local or unrecognizable this can be important to avoid unneces...

static void GetTrackMetaData(vector< CRef< CAnnotMetaData > > &data, const string &accession, const string &assembly, const string &context)

virtual CConstIRef< IAppJobProgress > GetProgress()=0

return progress object, the function shall be synchronized internally.

ICanceled * x_GetICanceled()

static CAppJobDispatcher & GetInstance()

virtual CConstIRef< IAppJobError > GetError()=0

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

virtual bool IsCanceled() const override

virtual CRef< CObject > GetResult()=0

Returns the Job Result.

bool DeleteJob(TJobID job_id)

when a Job is deleted the listener is not notified

EJobState

Job states (describe FSM)

virtual string GetDescr() const =0

Returns a human readable description of the Job (optional)

virtual EJobState Run()=0

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

@ eEngine_UnknownJob

the job is not registered in the Engine

@ eUnknownJob

Job record lost.

string GetSeqIdString(bool with_version=false) const

Return seqid string with optional version for text seqid type.

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.

double Elapsed(void) const

Return time elapsed since first Start() or last Restart() call (in seconds).

void Stop(void)

Suspend the timer.

string AsSmartString(CTimeSpan::ESmartStringPrecision precision, ERound rounding, CTimeSpan::ESmartStringZeroMode zero_mode=CTimeSpan::eSSZ_SkipZero) const

Transform elapsed time to "smart" string.

void Start(void)

Start the timer.

#define NCBI_GUIWIDGETS_SEQGRAPHIC_EXPORT

void SleepMilliSec(unsigned long ml_sec, EInterruptOnSignal onsignal=eRestartOnSignal)

Defines: CTimeFormat - storage class for time format.

Defines NCBI C++ API for timing-and-logging, classes, and macros.

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