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NCBI C++ ToolKit: CAlignedFeatureGraph Class Reference

Search Toolkit Book for CAlignedFeatureGraph

#include <gui/widgets/aln_multiple/feature_graph.hpp>

CAlignedFeatureGraph () CAlignedFeatureGraph (TMappedFeatLocs &feat_locs, objects::CScope &scope, const string &label, bool link_genes) virtual ~CAlignedFeatureGraph () virtual void x_Init (TMappedFeatLocs &feat_locs, objects::CScope &scope, const string &label, bool link_genes) void x_Init (CSeqGlyph::TObjects &glyphs, objects::CScope &scope, const string &label, bool link_genes) void x_Clear () void x_Layout () void x_SimpleLayout (TFeatRecPtrs &feat_recs) void x_LinkedLayout (TFeatRecPtrs &feat_recs) void x_GatherCluster (SFeatRec &feat_rec, TFeatRecPtrs &cluster) void x_GetRecsSortedByLength (const TFeatList &input, vector< TFeatRecPtrLenPair > &pairs) void x_PlaceCluster (TFeatRecPtrs &cluster) bool x_mRNA_CDS_ToBePlaced (const objects::CSeq_feat &feat) void x_TryPlaceCDSFeature (SFeatRec &rec) void x_PlaceFeature (SFeatRec &rec) void x_RenderFeature (CGlPane &pane, const SFeatRec &rec, int layer, TModelUnit top, TModelUnit bottom) virtual string x_GetTooltip (const SFeatRec &rec) virtual void Render (CGlPane &pane) virtual TVPPoint PreferredSize () virtual bool NeedTooltip (CGlPane &pane, int vp_x, int vp_y) virtual string GetTooltip () CObjectEx (void) virtual ~CObjectEx (void) 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 CWeakObject (void) virtual ~CWeakObject (void) CPtrToObjectProxy * GetPtrProxy (void) const Get pointer to proxy object containing pointer to this object. More...
CRenderableImpl () CRenderableImpl. More...
virtual ~CRenderableImpl () virtual TVPRect GetVPRect () const virtual void SetVPRect (const TVPRect &rc) virtual TModelRect GetModelRect () const virtual void SetModelRect (const TModelRect &rc) virtual bool IsVisible () virtual void SetVisible (bool set) virtual void SetOrder (int order) virtual int GetOrder () const virtual ~IRenderable (void) ◆ TClusters ◆ TColl ◆ TCollVector ◆ TFeatList ◆ TFeatRecPtrLenPair ◆ TFeatRecPtrs ◆ TFeatRecs ◆ TFeatToRecFlag ◆ TLayers ◆ TMappedFeatLocs ◆ CAlignedFeatureGraph() [1/2] ◆ CAlignedFeatureGraph() [2/2] ◆ ~CAlignedFeatureGraph() CAlignedFeatureGraph::~CAlignedFeatureGraph ( ) virtual ◆ GetTooltip() string CAlignedFeatureGraph::GetTooltip ( void ) virtual ◆ NeedTooltip()

Reimplemented from CRenderableImpl.

Definition at line 1006 of file feature_graph.cpp.

References _ASSERT, CGlPane::Close(), CAlignedFeatureGraph::SFeatRec::GetLocation(), CGlPane::GetScaleX(), CSeq_loc::GetTotalRange(), kTootipPix, m_LayerH, m_Layers, m_TooltipRec, CRenderableImpl::m_VPRect, NON_CONST_ITERATE, NULL, CGlPane::OpenOrtho(), CGlRect< T >::PtInRect(), r(), CGlRect< T >::Top(), and CGlPane::UnProjectX().

◆ PreferredSize() TVPPoint CAlignedFeatureGraph::PreferredSize ( ) virtual ◆ Render() void CAlignedFeatureGraph::Render ( CGlPane & pane ) virtual

Implements IRenderable.

Definition at line 854 of file feature_graph.cpp.

References IRender::BlendFunc(), CGlPane::Close(), IRender::Color3d(), IRender::Enable(), GetGl(), CGlPane::GetOffsetY(), i, m_LayerH, m_Layers, CRenderableImpl::m_ModelRect, CRenderableImpl::m_VPRect, CGlPane::OpenOrtho(), CGlPane::OpenPixels(), IRender::PolygonMode(), IRender::RectC(), CGlRect< T >::Top(), and x_RenderFeature().

◆ x_Clear() void CAlignedFeatureGraph::x_Clear ( void ) ◆ x_GatherCluster()

Definition at line 1307 of file feature_graph.cpp.

References map_checker< Container >::end(), CSeqFeatData::eSubtype_cdregion, CSeqFeatData::eSubtype_gene, CSeqFeatData::eSubtype_mRNA, map_checker< Container >::find(), GetBestCdsForMrna(), GetCdssForGene(), CAlignedFeatureGraph::SFeatRec::GetFeature(), GetMrnasForGene(), CConstRef< C, Locker >::GetPointer(), ITERATE, m_FeatToRecFlag, m_Scope, x_GetRecsSortedByLength(), and x_mRNA_CDS_ToBePlaced().

Referenced by x_LinkedLayout().

◆ x_GetRecsSortedByLength() ◆ x_GetTooltip()

Definition at line 1072 of file feature_graph.cpp.

References data, CLabel::eContent, CLabel::eDescription, fFGL_Content, NStr::fWithCommas, CBioseq_Handle::GetBioseqLength(), CSeq_feat_Base::GetData(), CSeqFeatData::GetFeatList(), CAlignedFeatureGraph::SFeatRec::GetFeature(), CSeq_loc::GetId(), CFeatList::GetItemBySubtype(), CLabel::GetLabel(), GetLabel(), GetLength(), COpenRange< Position >::GetLength(), CAlignedFeatureGraph::SFeatRec::GetLocation(), CSeq_feat_Base::GetLocation(), CRef< C, Locker >::GetPointer(), CSeq_feat_Base::GetProduct(), CFeatListItem::GetStoragekey(), CSeqFeatData::GetSubtype(), CSeq_loc::GetTotalRange(), NStr::IntToString(), CSeq_loc_Base::IsInt(), CSeq_loc_Base::IsPnt(), CSeq_feat_Base::IsSetProduct(), label, m_Scope, and r().

Referenced by GetTooltip().

◆ x_Init() [1/2] ◆ x_Init() [2/2] ◆ x_Layout() void CAlignedFeatureGraph::x_Layout ( )

Definition at line 1166 of file feature_graph.cpp.

References map_checker< Container >::clear(), CSeq_loc::GetTotalRange(), i, len, m_FeatRecs, m_FeatToRecFlag, m_LinkGenes, m_Occupied, NON_CONST_ITERATE, NULL, r(), s_ILPLonger(), x_LinkedLayout(), and x_SimpleLayout().

◆ x_LinkedLayout() void CAlignedFeatureGraph::x_LinkedLayout ( TFeatRecPtrs & feat_recs )

Definition at line 1226 of file feature_graph.cpp.

References CSeqFeatData::eSubtype_cdregion, CSeqFeatData::eSubtype_gene, CSeqFeatData::eSubtype_mRNA, CSeq_feat_Base::GetData(), CAlignedFeatureGraph::SFeatRec::GetFeature(), CSeqFeatData::GetSubtype(), i, m_FeatToRecFlag, x_GatherCluster(), x_mRNA_CDS_ToBePlaced(), x_PlaceCluster(), x_PlaceFeature(), and x_TryPlaceCDSFeature().

Referenced by x_Layout().

◆ x_mRNA_CDS_ToBePlaced() bool CAlignedFeatureGraph::x_mRNA_CDS_ToBePlaced ( const objects::CSeq_feat & feat ) ◆ x_PlaceCluster() void CAlignedFeatureGraph::x_PlaceCluster ( TFeatRecPtrs & cluster )

Definition at line 1431 of file feature_graph.cpp.

References _ASSERT, COpenRange< Position >::CombineWith(), map_checker< Container >::end(), map_checker< Container >::find(), CAlignedFeatureGraph::SFeatRec::GetFeature(), COpenRange< Position >::GetLength(), CAlignedFeatureGraph::SFeatRec::GetLocation(), i, CRangeCollection< Position >::IntersectingWith(), m_Clusters, m_FeatToRecFlag, m_Layers, m_Occupied, max(), min(), offset, r(), and CAlignedFeatureGraph::SFeatRec::SetClusterIndex().

Referenced by x_LinkedLayout().

◆ x_PlaceFeature() void CAlignedFeatureGraph::x_PlaceFeature ( SFeatRec & rec ) ◆ x_RenderFeature()

Definition at line 933 of file feature_graph.cpp.

References _ASSERT, IRender::Begin(), IRender::Color3d(), IRender::ColorC(), IRender::End(), CAlignedFeatureGraph::SFeatRec::GetClusterIndex(), GetColor(), CSeq_feat_Base::GetData(), CAlignedFeatureGraph::SFeatRec::GetFeature(), GetGl(), CAlignedFeatureGraph::SFeatRec::GetLocation(), CGlPane::GetOffsetX(), CGlPane::GetScaleX(), CSeqFeatData::GetSubtype(), CSeq_loc::GetTotalRange(), CGlPane::GetVisibleRect(), kLayerOffY, CGlRect< T >::Left(), m_Clusters, CAlignedFeatureGraph::SCluster::m_FirstLayer, CAlignedFeatureGraph::SCluster::m_LastLayer, CAlignedFeatureGraph::SCluster::m_Offset, min(), r(), IRender::Rectd(), CGlRect< T >::Right(), and IRender::Vertex2d().

Referenced by Render().

◆ x_SimpleLayout() void CAlignedFeatureGraph::x_SimpleLayout ( TFeatRecPtrs & feat_recs ) ◆ x_TryPlaceCDSFeature() void CAlignedFeatureGraph::x_TryPlaceCDSFeature ( SFeatRec & rec ) ◆ m_Clusters ◆ m_FeatRecs ◆ m_FeatToRecFlag ◆ m_Label string CAlignedFeatureGraph::m_Label protected ◆ m_LayerH int CAlignedFeatureGraph::m_LayerH protected ◆ m_Layers TLayers CAlignedFeatureGraph::m_Layers protected ◆ m_LinkGenes bool CAlignedFeatureGraph::m_LinkGenes protected ◆ m_Occupied ◆ m_Scope CRef<objects::CScope> CAlignedFeatureGraph::m_Scope protected ◆ m_TooltipRec SFeatRec* CAlignedFeatureGraph::m_TooltipRec protected

The documentation for this class was generated from the following files:

include/gui/widgets/aln_multiple/feature_graph.hpp
src/gui/widgets/aln_multiple/feature_graph.cpp

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