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NCBI C++ ToolKit: CSeqTextDataSource Class Reference
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CSeqTextDataSource implements Adapter design pattern. More...
#include <gui/widgets/seq_text/seq_text_ds.hpp>
CSeqTextDataSource (objects::CSeq_entry &sep, objects::CScope &scope) CSeqTextDataSource (objects::CBioseq_Handle handle, objects::CScope &scope) CSeqTextDataSource (objects::CSeq_loc &loc, objects::CScope &scope) virtual ~CSeqTextDataSource () void GetSeqData (TSeqPos start, TSeqPos stop, string &buffer, objects::SAnnotSelector *feat_sel=NULL, bool showFeatAsLower=false) void GetFeatureData (TSeqPos start_offset, TSeqPos stop_offset, CSeqTextConfig *cfg, ISeqTextGeometry *pParent, CSeqTextDefs::TSubtypeVector &subtypes, CSeqTextDefs::TSpliceSiteVector &splice_sites, CSeqTextDefs::TVariationGraphVector &variations) void GetSubtypesForAlternatingExons (TSeqPos start_offset, TSeqPos stop_offset, ISeqTextGeometry *pParent, CSeqTextDefs::TSubtypeVector &subtypes) void GetIntervalBreaks (TSeqPos start_offset, TSeqPos stop_offset, CSeqTextDefs::TSeqPosVector &breaks) void GetVariations (TSeqPos start_offset, TSeqPos stop_offset, CSeqTextDefs::TVariationGraphVector &variations) void RenderFeatureExtras (ISeqTextGeometry *pParent, CGlPane &pane, TSeqPos seq_start, TSeqPos seq_stop) TSeqPos GetDataLen () string GetTitle () TIdRef GetId () const TSeqPos SequencePosToSourcePos (TSeqPos sequence_pos, bool *found_in_source=NULL) TSeqPos SourcePosToSequencePos (TSeqPos source_pos) string GetToolTipForSourcePos (TSeqPos source_pos) vector< CConstRef< objects::CSeq_feat > > GetFeaturesAtPosition (TSeqPos source_pos) int FindSequenceFragment (const string &fragment, TSeqPos start_search) void FindSequenceFragmentList (const string &fragment, CSeqTextDefs::TSeqPosVector &locations, ICanceled *cancel) bool IsmRNASequence () const objects::CSeq_loc * GetLoc () const objects::CScope & GetScope () objects::CBioseq_Handle GetSeq () 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...
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
CSeqTextDataSource implements Adapter design pattern.
It adapts given CSeq_annot ot CSeq_align_set object by providing standard interface representing data as plain list of pair-wise alignments.
Definition at line 116 of file seq_text_ds.hpp.
◆ TAvailableSubtypeVector ◆ TIdRef ◆ TIntervalList ◆ CSeqTextDataSource() [1/3] CSeqTextDataSource::CSeqTextDataSource ( objects::CSeq_entry & sep, objects::CScope & scope ) ◆ CSeqTextDataSource() [2/3] CSeqTextDataSource::CSeqTextDataSource ( objects::CBioseq_Handle handle, objects::CScope & scope ) ◆ CSeqTextDataSource() [3/3] CSeqTextDataSource::CSeqTextDataSource ( objects::CSeq_loc & loc, objects::CScope & scope ) ◆ ~CSeqTextDataSource() CSeqTextDataSource::~CSeqTextDataSource ( ) virtual
Definition at line 120 of file seq_text_ds.cpp.
◆ ChooseBetterSubtype() int CSeqTextDataSource::ChooseBetterSubtype ( int subtype1, int subtype2 ) static ◆ FindSequenceFragment() ◆ FindSequenceFragmentList() ◆ GetDataLen() TSeqPos CSeqTextDataSource::GetDataLen ( )
Definition at line 402 of file seq_text_ds.cpp.
References GetLength(), m_Loc, and m_Scope.
Referenced by FindSequenceFragment(), FindSequenceFragmentList(), GetFeatureData(), GetFeaturesAtPosition(), CSequenceTextGraph::GetModelRect(), CSequenceTickGraph::GetModelRect(), CSeqTextPane::GetScrollAdjustmentForLastLineVariations(), CSequenceTickGraph::PreferredSize(), CSeqTextPane::STG_GetLineInfo(), CSeqTextPane::STG_GetSequenceByWindow(), CSeqTextPane::STG_ReportMouseOverPos(), and CSequenceTextGraph::x_RenderSequence().
◆ GetFeatureData() ◆ GetFeaturesAtPosition() ◆ GetId() ◆ GetIntervalBreaks() ◆ GetLoc() ◆ GetScope() CScope & CSeqTextDataSource::GetScope ( void ) ◆ GetSeq() objects::CBioseq_Handle CSeqTextDataSource::GetSeq ( void ) inline ◆ GetSeqData() ◆ GetSeqString() ◆ GetSubtypesForAlternatingExons() ◆ GetTitle() string CSeqTextDataSource::GetTitle ( void ) ◆ GetToolTipForSourcePos() string CSeqTextDataSource::GetToolTipForSourcePos ( TSeqPos source_pos ) ◆ GetVariations() ◆ IsmRNASequence() bool CSeqTextDataSource::IsmRNASequence ( ) ◆ RenderFeatureExtras() ◆ SequencePosToSourcePos() ◆ SourcePosToSequencePos() TSeqPos CSeqTextDataSource::SourcePosToSequencePos ( TSeqPos source_pos ) ◆ x_PopulateFeatureIterators() void CSeqTextDataSource::x_PopulateFeatureIterators ( ) protected ◆ m_ID TIdRef CSeqTextDataSource::m_ID protected ◆ m_Intervals
Definition at line 168 of file seq_text_ds.hpp.
Referenced by GetFeatureData(), GetFeaturesAtPosition(), GetSeqData(), GetSeqString(), GetSubtypesForAlternatingExons(), GetToolTipForSourcePos(), GetVariations(), RenderFeatureExtras(), SequencePosToSourcePos(), SourcePosToSequencePos(), and x_PopulateFeatureIterators().
◆ m_Loc CRef<objects::CSeq_loc> CSeqTextDataSource::m_Loc protected ◆ m_Scope CRef<objects::CScope> CSeqTextDataSource::m_Scope protected ◆ m_Sep ◆ m_SubjectHandle objects::CBioseq_Handle CSeqTextDataSource::m_SubjectHandle protected
The documentation for this class was generated from the following files:
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