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Showing content from http://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/doxyhtml/seqgraphic__genbank__ds_8cpp_source.html below:

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

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User-defined methods of the data storage class.

size_t GetSize(void) const

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

CAppJobNotification Notification send by CAppJobEventTranslator.

static void CalcGraphLevels(const string &annotName, objects::CScope &scope, const objects::CSeq_loc &loc, set< int > &levels)

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

Launch either a background or foreground job.

void SetGraphLevels(const string &annot)

vector< TJobID > m_ActiveJobs

all currently active jobs for this DS

CAppJobDispatcher::TJobID TJobID

objects::CScope & GetScope(void) const

Get the scope from the handle.

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

CEventHandler * m_JobListener

our listener to JobDispatcher events

void x_ForegroundJob(IAppJob &job)

virtual void ClearJobID(TJobID job_id)

TGraphLevels m_GraphLevels

Existing coverage graph levels.

virtual void DeleteAllJobs()

Remove waiting jobs from queue or cancel the unfinished jobs.

objects::CBioseq_Handle m_Handle

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

Jobs on thread pool.

virtual ISGDataSource * CreateDS(SConstScopedObject &object) const

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

virtual string GetExtensionLabel() const

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

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.

CRef< objects::CSeqVector > m_SeqVector

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

CSGSequenceDS.

bool IsAccGenomic(objects::CSeq_id::EAccessionInfo acc_info) const

string GetAcc_All() const

all accession info we can get in FASTA format

bool IsTraceAssembly() const

objects::CBioseq_Handle m_Handle

void GetSequence(TSeqPos from, TSeqPos to, string &buffer) const

retrieve a string representing the IUPAC characters for the sequence [from to].

bool IsRefSeqGene() const

string GetAcc_Best() const

this is more suitable for display purposes since the returned string will not always be good to recon...

objects::CSeq_id_Handle m_Best_idh

best id handle (obtained with sequence::GetId(..., sequence::eGetId_Best))

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

unsigned int TSeqPos

Type for sequence locations and lengths.

#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...

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.

static CAppJobDispatcher & GetInstance()

virtual CConstIRef< IAppJobError > GetError()=0

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

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)

TJobID StartJob(IAppJob &job, const string &engine_name, IEngineParams *params=NULL)

Starts a Job on the specified engine in "passive mode" - no notifications or progress reports will be...

virtual EJobState Run()=0

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

virtual bool Send(CEvent *evt, EDispatch disp_how=eDispatch_Default, int pool_name=ePool_Default)

Sends an event synchronously.

@ eEngine_UnknownJob

the job is not registered in the Engine

@ eUnknownJob

Job record lost.

EAccessionInfo

For IdentifyAccession (below)

static string GetStringDescr(const CBioseq &bioseq, EStringFormat fmt)

@ eAcc_refseq_wgs_intermed

@ eContent

Untagged human-readable accession or the like.

const CSeq_id & GetId(const CSeq_loc &loc, CScope *scope)

If all CSeq_ids embedded in CSeq_loc refer to the same CBioseq, returns the first CSeq_id found,...

@ eGetId_Best

return the "best" gi (uses FindBestScore(), with CSeq_id::CalculateScore() as the score function

CBioseq_Handle GetBioseqHandle(const CSeq_id &id)

Get bioseq handle by seq-id.

TClass GetClass(void) const

bool IsSetClass(void) const

@ eCoding_Iupac

Set coding to printable coding (Iupacna or Iupacaa)

TObjectType * GetPointer(void) const 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 bool EqualNocase(const CTempString s1, SIZE_TYPE pos, SIZE_TYPE n, const char *s2)

Case-insensitive equality of a substring with another string.

const TKeywords & GetKeywords(void) const

Get the Keywords member data.

bool CanGetKeywords(void) const

Check if it is safe to call GetKeywords method.

const TDb & GetDb(void) const

Get the Db member data.

bool IsGeneral(void) const

Check if variant General is selected.

const TGeneral & GetGeneral(void) const

Get the variant data.

@ eClass_pop_set

population study

@ eClass_phy_set

phylogenetic study

@ eClass_mut_set

set of mutations

@ eClass_eco_set

ecological sample study

const TGenbank & GetGenbank(void) const

Get the variant data.

@ e_Genbank

GenBank specific info.

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