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NCBI C++ ToolKit: include/gui/widgets/seq_graphic/seqgraphic_genbank_ds.hpp Source File

1 #ifndef GUI_WIDGETS_SEQ_GRAPHIC___SEQGRAPHIC_GENBANK_DS__HPP 2 #define GUI_WIDGETS_SEQ_GRAPHIC___SEQGRAPHIC_GENBANK_DS__HPP 59  CSGGenBankDS

(objects::CScope& scope,

const

objects::CSeq_id&

id

);

63  bool

IsRefSeq()

const

;

66  void

SetDepth(

int depth

);

67  int

GetDepth()

const

;

69  void

SetAdaptive(

bool

flag);

70  bool

GetAdaptive()

const

;

73 

objects::CBioseq_Handle& GetBioseqHandle(

void

);

75  const

objects::CBioseq_Handle& GetBioseqHandle(

void

)

const

;

78 

objects::CScope&

GetScope

(

void

)

const

;

83  virtual void

ClearJobID(

TJobID

job_id);

84  bool

IsJobNeeded(

TJobID

job_id)

const

;

85  virtual bool

AllJobsFinished()

const

;

87  virtual void

DeleteAllJobs();

97  void

SetGraphLevels(

const string

& annot);

102  void

x_ForegroundJob(

IAppJob

& job);

105  TJobID

x_BackgroundJob(

IAppJob

& job,

int

report_period,

const string

& pool);

110  const string

& pool =

"ObjManagerEngine"

);

152  CSGSequenceDS

(objects::CScope& scope,

const

objects::CSeq_id&

id

);

156 

objects::CBioseq_Handle GetBioseqHandle(

void

)

const

;

158

objects::CSeq_id_Handle GetBestIdHandle()

const

;

161 

objects::CScope&

GetScope

(

void

)

const

;

163  const

objects::CSeqVector& GetSeqVector(

void

)

const

;

165  TSeqPos

GetSequenceLength()

const

;

174  string

GetAcc_Best()

const

;

176  string

GetAcc_All()

const

;

178  bool

IsAccGenomic(objects::CSeq_id::EAccessionInfo acc_info)

const

;

179  bool

IsTraceAssembly()

const

;

180  bool

IsPopSet()

const

;

181  bool

IsRefSeq()

const

;

205  virtual string

GetExtensionIdentifier()

const

;

206  virtual string

GetExtensionLabel()

const

;

210  virtual bool

IsSharable()

const

;

Default seqgraphic data source implementation.

CIRef< ICoordMapper > m_Mapper

coordinate mapper between mapped features coord. and sequence coord.

bool IsJobNeeded(TJobID job_id) const

bool m_Adaptive

adaptive/exact annot selector

int m_Depth

annotation resolving depth

vector< TJobID > m_ActiveJobs

all currently active jobs for this DS

CAppJobDispatcher::TJobID TJobID

void SetCoordMapper(ICoordMapper *mapper)

objects::CScope & GetScope(void) const

Get the scope from the handle.

virtual bool AllJobsFinished() const

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

CSGGenBankDS & operator=(const CSGGenBankDS &)

CEventHandler * m_JobListener

our listener to JobDispatcher events

void SetJobListener(CEventHandler *listener)

Set JobDispatcher listener.

objects::CBioseq_Handle & GetBioseqHandle(void)

Get the underlying bioseq handle.

void SetDepth(int depth)

Set the annotation selector resolving depth.

TGraphLevels m_GraphLevels

Existing coverage graph levels.

objects::CBioseq_Handle m_Handle

CSGGenBankDS(const CSGGenBankDS &)

void SetAdaptive(bool flag)

CRef< objects::CSeqVector > m_SeqVector

objects::CScope & GetScope(void) const

Get the scope from the handle.

TSeqPos GetSequenceLength() const

const objects::CSeqVector & GetSeqVector(void) const

objects::CBioseq_Handle m_Handle

objects::CBioseq_Handle GetBioseqHandle(void) const

Get the underlying bioseq handle.

objects::CSeq_id_Handle m_Best_idh

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

objects::CSeq_id_Handle GetBestIdHandle() const

ICoordMapper interface for converting location between two coordinate systems.

IExtension IExtension interface represents an abstract pluggable component.

static unsigned char depth[2 *(256+1+29)+1]

SBlastSequence GetSequence(const objects::CSeq_loc &sl, EBlastEncoding encoding, objects::CScope *scope, objects::ENa_strand strand=objects::eNa_strand_plus, ESentinelType sentinel=eSentinels, std::string *warnings=NULL)

Retrieves a sequence using the object manager.

unsigned int TSeqPos

Type for sequence locations and lengths.

NCBI_XOBJUTIL_EXPORT string GetTitle(const CBioseq_Handle &hnd, TGetTitleFlags flags=0)

void Reset(void)

Reset reference object.

#define END_NCBI_SCOPE

End previously defined NCBI scope.

#define BEGIN_NCBI_SCOPE

Define ncbi namespace.

#define NCBI_GUIWIDGETS_SEQGRAPHIC_EXPORT

Defines to provide correct exporting from DLLs in Windows.

static bool IsRefSeqGene(const CBioseq_Handle &bsh)

Multi-threading – mutexes; rw-locks; semaphore.

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