Search Toolkit Book for CBinsDS
#include <gui/packages/pkg_snp/bins/bins_ds.hpp>
Inheritance diagram for CBinsDS:
Collaboration diagram for CBinsDS:
Public Member Functions | |
| CBinsDS (objects::CScope &scope, const objects::CSeq_id &id) | |
| CBinsDS. More... | |
| void | SetName (const string &) |
| void | LoadData (const TSeqRange &range, TModelUnit scale, bool isSeqView) |
| Public Member Functions inherited from CSGGenBankDS | |
| CSGGenBankDS (objects::CScope &scope, const objects::CSeq_id &id) | |
| virtual | ~CSGGenBankDS () |
| bool | IsRefSeq () const |
| void | SetDepth (int depth) |
| Set the annotation selector resolving depth. More... | |
| int | GetDepth () const |
| void | SetAdaptive (bool flag) |
| bool | GetAdaptive () const |
| objects::CBioseq_Handle & | GetBioseqHandle (void) |
| Get the underlying bioseq handle. More... | |
| const objects::CBioseq_Handle & | GetBioseqHandle (void) const |
| objects::CScope & | GetScope (void) const |
| Get the scope from the handle. More... | |
| void | SetJobListener (CEventHandler *listener) |
| Set JobDispatcher listener. More... | |
| virtual void | ClearJobID (TJobID job_id) |
| bool | IsJobNeeded (TJobID job_id) const |
| virtual bool | AllJobsFinished () const |
| virtual void | DeleteAllJobs () |
| Remove waiting jobs from queue or cancel the unfinished jobs. More... | |
| void | SetCoordMapper (ICoordMapper *mapper) |
| void | SetGraphLevels (const string &annot) |
| Public Member Functions inherited from CObjectEx | |
| CObjectEx (void) | |
| virtual | ~CObjectEx (void) |
| Public Member Functions inherited from CObject | |
| CObject (void) | |
| Constructor. More... | |
| CObject (const CObject &src) | |
| Copy constructor. More... | |
| virtual | ~CObject (void) |
| Destructor. More... | |
| CObject & | operator= (const CObject &src) THROWS_NONE |
| Assignment operator. More... | |
| bool | CanBeDeleted (void) const THROWS_NONE |
| Check if object can be deleted. More... | |
| bool | IsAllocatedInPool (void) const THROWS_NONE |
| Check if object is allocated in memory pool (not system heap) More... | |
| bool | Referenced (void) const THROWS_NONE |
| Check if object is referenced. More... | |
| bool | ReferencedOnlyOnce (void) const THROWS_NONE |
| Check if object is referenced only once. More... | |
| void | AddReference (void) const |
| Add reference to object. More... | |
| void | RemoveReference (void) const |
| Remove reference to object. More... | |
| void | ReleaseReference (void) const |
| Remove reference without deleting object. More... | |
| virtual void | DoNotDeleteThisObject (void) |
| Mark this object as not allocated in heap – do not delete this object. More... | |
| virtual void | DoDeleteThisObject (void) |
| Mark this object as allocated in heap – object can be deleted. More... | |
| void * | operator new (size_t size) |
| Define new operator for memory allocation. More... | |
| void * | operator new[] (size_t size) |
| Define new[] operator for 'array' memory allocation. More... | |
| void | operator delete (void *ptr) |
| Define delete operator for memory deallocation. More... | |
| void | operator delete[] (void *ptr) |
| Define delete[] operator for memory deallocation. More... | |
| void * | operator new (size_t size, void *place) |
| Define new operator. More... | |
| void | operator delete (void *ptr, void *place) |
| Define delete operator. More... | |
| void * | operator new (size_t size, CObjectMemoryPool *place) |
| Define new operator using memory pool. More... | |
| void | operator delete (void *ptr, CObjectMemoryPool *place) |
| Define delete operator. More... | |
| virtual void | DebugDump (CDebugDumpContext ddc, unsigned int depth) const |
| Define method for dumping debug information. More... | |
| Public Member Functions inherited from CDebugDumpable | |
| CDebugDumpable (void) | |
| virtual | ~CDebugDumpable (void) |
| void | DebugDumpText (ostream &out, const string &bundle, unsigned int depth) const |
| void | DebugDumpFormat (CDebugDumpFormatter &ddf, const string &bundle, unsigned int depth) const |
| void | DumpToConsole (void) const |
| Public Member Functions inherited from CWeakObject | |
| CWeakObject (void) | |
| virtual | ~CWeakObject (void) |
| CPtrToObjectProxy * | GetPtrProxy (void) const |
| Get pointer to proxy object containing pointer to this object. More... | |
| Public Member Functions inherited from ISGDataSource | |
| virtual | ~ISGDataSource () |
Static Public Member Functions | |
| static void | GetTrackNames (SConstScopedObject &object, TAnnotNameTitleMap &names, const TSeqRange &range, const ILayoutTrackFactory::SExtraParams &) |
| Static Public Member Functions inherited from CSGDataSource | |
| static void | SetBackgroundJob (bool flag) |
| static bool | IsBackgroundJob () |
| Static Public Member Functions inherited from CObject | |
| static NCBI_XNCBI_EXPORT void | ThrowNullPointerException (void) |
| Define method to throw null pointer exception. More... | |
| static NCBI_XNCBI_EXPORT void | ThrowNullPointerException (const type_info &type) |
| static EAllocFillMode | GetAllocFillMode (void) |
| static void | SetAllocFillMode (EAllocFillMode mode) |
| static void | SetAllocFillMode (const string &value) |
| Set mode from configuration parameter value. More... | |
| Static Public Member Functions inherited from CDebugDumpable | |
| static void | EnableDebugDump (bool on) |
Private Attributes | |
| string | m_Name |
Additional Inherited Members | |
| Public Types inherited from CSGGenBankDS | |
| typedef CAppJobDispatcher::TJobID | TJobID |
| typedef int | TJobToken |
| Public Types inherited from CObject | |
| enum | EAllocFillMode { eAllocFillNone = 1 , eAllocFillZero , eAllocFillPattern } |
| Control filling of newly allocated memory. More... | |
| typedef CObjectCounterLocker | TLockerType |
| Default locker type for CRef. More... | |
| typedef atomic< Uint8 > | TCounter |
| Counter type is CAtomiCounter. More... | |
| typedef Uint8 | TCount |
| Alias for value type of counter. More... | |
| Public Types inherited from ISGDataSource | |
| typedef map< string, string > | TAnnotNameTitleMap |
| List of annotations with the corresponding titles. More... | |
| Static Public Attributes inherited from CObject | |
| static const TCount | eCounterBitsCanBeDeleted = 1 << 0 |
| Define possible object states. More... | |
| static const TCount | eCounterBitsInPlainHeap = 1 << 1 |
| Heap signature was found. More... | |
| static const TCount | eCounterBitsPlaceMask |
| Mask for 'in heap' state flags. More... | |
| static const int | eCounterStep = 1 << 2 |
| Skip over the "in heap" bits. More... | |
| static const TCount | eCounterValid = TCount(1) << (sizeof(TCount) * 8 - 2) |
| Minimal value for valid objects (reference counter is zero) Must be a single bit value. More... | |
| static const TCount | eCounterStateMask |
| Valid object, and object in heap. More... | |
| Protected Types inherited from CSGGenBankDS | |
| typedef set< int > | TGraphLevels |
| Protected Member Functions inherited from CSGGenBankDS | |
| void | x_ForegroundJob (IAppJob &job) |
| TJobID | x_BackgroundJob (IAppJob &job, int report_period, const string &pool) |
| Jobs on thread pool. More... | |
| TJobID | x_LaunchJob (IAppJob &job, int report_period=1, const string &pool="ObjManagerEngine") |
| Launch either a background or foreground job. More... | |
| Protected Member Functions inherited from CObject | |
| virtual void | DeleteThis (void) |
| Virtual method "deleting" this object. More... | |
| Protected Member Functions inherited from CWeakObject | |
| void | CleanWeakRefs (void) const |
| Method cleaning all CWeakRefs referencing at this moment to the object After calling to this method all existing CWeakRefs referencing to the object will return NULL, so it effectively will be equal to deleting the object. More... | |
| Protected Attributes inherited from CSGGenBankDS | |
| objects::CBioseq_Handle | m_Handle |
| CEventHandler * | m_JobListener |
| our listener to JobDispatcher events More... | |
| vector< TJobID > | m_ActiveJobs |
| all currently active jobs for this DS More... | |
| int | m_Depth |
| annotation resolving depth More... | |
| bool | m_Adaptive |
| adaptive/exact annot selector More... | |
| CIRef< ICoordMapper > | m_Mapper |
| coordinate mapper between mapped features coord. and sequence coord. More... | |
| TGraphLevels | m_GraphLevels |
| Existing coverage graph levels. More... | |
| Static Protected Attributes inherited from CSGDataSource | |
| static bool | m_Background = true |
Detailed Description
Definition at line 60 of file bins_ds.hpp.
Constructor & Destructor Documentation
◆ CBinsDS()
| CBinsDS::CBinsDS | ( | objects::CScope & | scope, |
| const objects::CSeq_id & | id | ||
| ) |
Definition at line 323 of file bins_ds.cpp.
Member Function Documentation
◆ GetTrackNames()
|
static |
Definition at line 327 of file bins_ds.cpp.
References CSeq_annot_Base::C_Data::e_Seq_table, eNa_strand_unknown, CAnnotTypes_CI::GetAnnotNames(), CSeqUtils::GetAnnotSelector(), ITERATE, ILayoutTrackFactory::SExtraParams::m_Adaptive, ILayoutTrackFactory::SExtraParams::m_Annots, ILayoutTrackFactory::SExtraParams::m_Level, names, compile_time_bits::range(), SAnnotSelector::SetAnnotType(), SAnnotSelector::SetCollectNames(), and CSeqUtils::SetResolveDepth().
Referenced by CBinsTrackFactory::CreateTracks().
◆ LoadData()
| void CBinsDS::LoadData | ( | const TSeqRange & | range, |
| TModelUnit | scale, | ||
| bool | isSeqView | ||
| ) |
Definition at line 358 of file bins_ds.cpp.
References CBinsJob::SParams::bAdaptiveSelector, CBinsJob::SParams::binWidth, NSnpGui::c_BinWidth, CBinsJob::SParams::depth, CBinsJob::SParams::isSeqView, CSGGenBankDS::m_Adaptive, CSGGenBankDS::m_Depth, CSGGenBankDS::m_Handle, m_Name, CBinsJob::SParams::name, compile_time_bits::range(), CRef< C, Locker >::Reset(), CBinsJob::SParams::scale, and CSGGenBankDS::x_LaunchJob().
Referenced by CBinsTrack::x_UpdateData().
◆ SetName()
Definition at line 353 of file bins_ds.cpp.
References m_Name.
Referenced by CBinsTrackFactory::CreateTracks().
Member Data Documentation
◆ m_Name
|
private |
Definition at line 77 of file bins_ds.hpp.
Referenced by LoadData(), and SetName().
The documentation for this class was generated from the following files:
- include/gui/packages/pkg_snp/bins/bins_ds.hpp
- src/gui/packages/pkg_snp/bins/bins_ds.cpp
