NCBI C++ ToolKit
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CGeneGroup Class Reference

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CGeneGroup is a subclass of CLayoutGroup contains gene, RNA, cds, and Exon features. More...

#include <gui/widgets/seq_graphic/gene_model_group.hpp>

+ Inheritance diagram for CGeneGroup:
+ Collaboration diagram for CGeneGroup:

Public Types

enum  EGene { eGene_Shown , eGene_ShowLabelOnly , eGene_Hidden }
 
- Public Types inherited from CLayoutGroup
typedef ILayoutPolicy::TObjectList TObjectList
 
- Public Types inherited from CSeqGlyph
enum  ENeighbours { eNghbrs_None = 0x0 , eNghbrs_Left = 0x1 , eNghbrs_Right = 0x2 , eNghbrs_Both = 0x3 }
 
typedef vector< CHTMLActiveAreaTAreaVector
 
typedef list< CRef< CSeqGlyph > > TObjects
 
typedef list< CConstRef< CSeqGlyph > > TConstObjects
 
- 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< Uint8TCounter
 Counter type is CAtomiCounter. More...
 
typedef Uint8 TCount
 Alias for value type of counter. More...
 
- Public Types inherited from IObjectBasedGlyph
typedef vector< TSeqRangeTIntervals
 

Public Member Functions

 CGeneGroup ()
 
virtual ~CGeneGroup (void)
 
void SetShowGene (bool flag)
 
void HideGeneAndLabel ()
 CGeneGroup inline methods. More...
 
CSeqGlyph interface implementation
virtual void Update (bool layout_only)
 CGeneGroup implementations. More...
 
virtual TSeqRange GetRange (void) const
 Get gene feature range instead. More...
 
virtual bool Accept (IGlyphVisitor *visitor)
 Interface for accepting an IGlyphVisitor. More...
 
virtual void GetHTMLActiveAreas (TAreaVector *p_areas) const
 Get html active areas. More...
 
IObjectBasedGlyph interface implement
virtual const objects::CSeq_loc & GetLocation () const
 access the position of this object. More...
 
virtual CConstRef< CObjectGetObject (TSeqPos pos) const
 access our core component - we wrap an object(s) of some sort. More...
 
virtual void GetObjects (vector< CConstRef< CObject > > &objs) const
 retrieve CObjects corresponding to this CSeqGlyph. More...
 
virtual bool HasObject (CConstRef< CObject > obj) const
 check if the wrapped object(s) is the one. More...
 
virtual string GetSignature () const
 return signature for this glyph. More...
 
virtual const TIntervalsGetIntervals () const
 access sub-intervals (if any). More...
 
- Public Member Functions inherited from CLayoutGroup
 CLayoutGroup (ELinkedFeatDisplay LinkedFeat=ELinkedFeatDisplay::eLFD_Default)
 
virtual ~CLayoutGroup (void)
 
void SetConfig (const CBoundaryParams *conf)
 Set composition boundary parameters. More...
 
void SetLayoutPolicy (ILayoutPolicy *policy)
 Set policy on how to deploy the layout of its children. More...
 
void UpdateBoundingBox ()
 update group's bounding box only. More...
 
void UpdateLayout ()
 update group's bounding box only, and its parent layout. More...
 
bool AllChildrenSameType () const
 Return true if there are 0 or 1 children, or all children are features of the same type (e.g. More...
 
void SetAsMaster (CRef< CSeqGlyph > master)
 master glyph has some special meaning (e.g. More...
 
bool IsMaster (const CSeqGlyph *glyph) const
 
void HideMaster (bool hidden=true)
 
bool IsMasterHidden () const
 
void SetLinkedFeat (ELinkedFeatDisplay LinkedFeat)
 
ELinkedFeatDisplay GetLinkedFeat () const
 
const TObjectListGetChildren () const
 CLayoutGroup inline methods. More...
 
TObjectListGetChildren ()
 
size_t GetChildrenNum () const
 Get total number of children. More...
 
CConstRef< CSeqGlyphGetChild (int idx) const
 Get the layout object at index 'idx'. More...
 
CRef< CSeqGlyphGetChild (int idx)
 Get the layout object at index 'idx'. More...
 
int GetIndex (const CSeqGlyph *obj) const
 Get the child index. More...
 
bool Remove (CSeqGlyph *obj)
 Remove a layout object. More...
 
bool Replace (CSeqGlyph *obj, int idx)
 Replace a child at index 'idx'. More...
 
void Insert (int at, CSeqGlyph *obj)
 Insert a layout object before the given index. More...
 
void Insert (const CSeqGlyph *at_obj, CSeqGlyph *obj)
 Insert a layout object before the given layout object. More...
 
void InsertAft (const CSeqGlyph *at_obj, CSeqGlyph *obj)
 Insert a layout object after the given layout object. More...
 
void PushBack (CSeqGlyph *obj)
 Append a layout object to the end. More...
 
void PushFront (CSeqGlyph *obj)
 
void Set (const TObjectList &objs)
 
void Append (TObjectList &objs)
 
TObjectListSetChildren ()
 
void Clear ()
 
virtual CRef< CSeqGlyphHitTest (const TModelPoint &p)
 Hit testing. More...
 
virtual bool HitTestHor (TSeqPos x, const CObject *obj)
 
virtual bool Intersects (const TModelRect &rect, TConstObjects &objs) const
 Intersect testing. More...
 
- Public Member Functions inherited from CSeqGlyph
 CSeqGlyph ()
 
virtual ~CSeqGlyph ()
 
virtual bool NeedTooltip (const TModelPoint &, ITooltipFormatter &, string &) const
 Check if need to show tooltip. More...
 
virtual void GetTooltip (const TModelPoint &, ITooltipFormatter &tt, string &t_title) const
 Get the tooltip if available. More...
 
virtual bool SetSelected (bool flag)
 Select or deselect this glyph. More...
 
virtual void SetHideLabel (bool)
 Force to hide label. More...
 
virtual bool HasSideLabel () const
 Query if there is label and label is on the side. More...
 
virtual bool IsClickable () const
 Query if this glyph is clickable. More...
 
virtual bool LessBySeqPos (const CSeqGlyph &obj) const
 compare this object to another based on glyph sequence position. More...
 
bool LessByPos (const CSeqGlyph &obj) const
 compare this object to another, based on glyph geometry position. More...
 
bool LessBySeqSize (const CSeqGlyph &obj) const
 compare this object to another, based on sequence size. More...
 
bool LessBySize (const CSeqGlyph &obj) const
 compare this object to another, based on geometry size. More...
 
void Draw () const
 render the layout. More...
 
TModelRect GetModelRect () const
 get the bounding box. More...
 
bool IsIn (const TModelPoint &p) const
 Hit test for points in PARENT COORD. More...
 
bool IsIn (TModelUnit x, TModelUnit y) const
 
bool IsInHor (TModelUnit x) const
 
void SetRender (IGlyphRenderer *renderer)
 set customized renderer for this layout objects. More...
 
void SetRenderingContext (CRenderingContext *context)
 Set the rendering context. More...
 
const CRenderingContextGetRenderingContext () const
 Get the rendering context. More...
 
void SetTearline (size_t Tearline)
 tearline factor – used to limit a list of glyphs More...
 
size_t GetTearline () const
 
void SetTearlineText (const string &sTearlineText)
 tearline text – if set, is appended to the glyph name (does not naffect processing otherwise) More...
 
string GetTearlineText () const
 
void SetRowNum (size_t cur_row)
 
size_t GetRowNum () const
 
void SetVisible (size_t v)
 
size_t GetVisible () const
 
int GetLevel () const
 
void SetLevel (int Level)
 
virtual string GetPName () const
 persistent name of the glyph should not depend on the instance of the glyph, but should uniquely reflect its contents so two glyphs having the same contents will have the same name currently used to track isDrawn() status for expandable glyphs default implementation returns an empty string implementations exist for CFeatGlyph (name of the contained feature) and CLayoutGroup (concatenation of all sorted children names) More...
 
float GetFadeFactor () const
 
virtual bool OnLeftDown (const TModelPoint &)
 
virtual bool OnLeftUp (const TModelPoint &)
 
virtual bool OnLeftDblClick (const TModelPoint &)
 
virtual bool OnContextMenu (wxContextMenuEvent &event)
 
bool IsSelected () const
 
bool IsHighlighted () const
 
CRgbaColorGetHighlightsColor () const
 
virtual TModelUnit GetHeight () const
 
virtual TModelUnit GetWidth () const
 
virtual TModelUnit GetLeft () const
 
virtual TModelUnit GetTop () const
 
virtual TModelUnit GetRight () const
 
virtual TModelUnit GetBottom () const
 
const TModelPointGetPos () const
 
void GetPosInWorld (TModelPoint &pos) const
 Get top left position in world coordinate. More...
 
const CSeqGlyphGetParent (void) const
 
CSeqGlyphGetParent (void)
 
ENeighbours GetNeighbours () const
 
void SetHighlighted (bool flag)
 
void SetHighlightsColor (const CRgbaColor &hl_color)
 
void SetHighlightsColor (const string &hl_color_str)
 
virtual void SetWidth (TModelUnit w)
 
virtual void SetHeight (TModelUnit h)
 
virtual void SetLeft (TModelUnit l)
 
virtual void SetTop (TModelUnit b)
 
virtual void SetPos (const TModelPoint &upper_left)
 
void SetParent (CSeqGlyph *p)
 
CSeqGlyphSetParent (void)
 
void SetNeighbours (ENeighbours neighbours)
 
- 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...
 
CObjectoperator= (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)
 
CPtrToObjectProxyGetPtrProxy (void) const
 Get pointer to proxy object containing pointer to this object. More...
 
- Public Member Functions inherited from IObjectBasedGlyph
virtual ~IObjectBasedGlyph ()
 

Protected Member Functions

bool x_ShowGeneLabel () const
 
TModelUnit x_GetLabelHeight () const
 Returns the height of the label with margin included. More...
 
CSeqGlyph virtual methods.
virtual void x_Draw () const
 The default renderer for this layout object. More...
 
- Protected Member Functions inherited from CLayoutGroup
void x_DrawBoundary () const
 
bool x_isDrawn () const
 determines whether the glyph should be drawn or not at all (currently children of unselected parents when m_LinkedFeat is set to "Expandable") More...
 
bool x_HasExpandedChildren () const
 
virtual void x_UpdateBoundingBox ()
 Update the bounding box assuming children's sizes are fixed if any. More...
 
virtual void x_DrawHighlight () const
 override x_DrawHighlight() to do nothing. More...
 
- Protected Member Functions inherited from CSeqGlyph
void x_DrawInnerLabelColumns (TModelUnit base, const string &label, const CRgbaColor &color, const CGlTextureFont &font, bool side_label_visible) const
 
void x_DrawInnerLabels (TModelUnit base, const string &label, const CRgbaColor &color, const CGlTextureFont &font, bool side_label_visible, bool inside_only, vector< TModelRange > *labels_ranges=nullptr, TSeqRange *interval=nullptr, bool XOR_mode=false) const
 
void x_DrawTruncatedLabel (const string &label, const CGlTextureFont &font, TModelUnit width, TModelUnit x, TModelUnit y, vector< TModelRange > *labels_ranges=nullptr) const
 
void x_DrawException () const
 Draw a shading background to indicate exception. More...
 
virtual void x_OnLayoutChanged ()
 update the layout. More...
 
void x_Parent2Local (TModelPoint &pnt) const
 Transform the coordiante from parent coord. to local coord. More...
 
void x_Parent2Local (TModelUnit &, TModelUnit &y) const
 Transform the coordiante from parent coord. to local coord. More...
 
void x_Parent2Local (TModelRect &rect) const
 Transform the coordiante from parent coord. to local coord. More...
 
void x_World2Local (TModelPoint &p) const
 Transform the coordiante from world coord. to local coord. More...
 
void x_World2Local (TModelUnit &x, TModelUnit &y) const
 
void x_Local2World (TModelPoint &p) const
 Transform the coordiantes from local coord. to world coord. More...
 
void x_Local2World (TModelUnit &x, TModelUnit &y) const
 
void x_InitHTMLActiveArea (CHTMLActiveArea &area) const
 initialize the basic information for a given active area. More...
 
bool x_Visible_V () const
 is this glyph visible in vertical direction? More...
 
template<class T >
bool x_IntersectVisible (const CRange< T > &SeqRange, T &from, T &to) const
 
- 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...
 

Private Member Functions

const CFeatGlyphx_GetFirstFeat () const
 

Private Attributes

EGene m_ShowGene
 

Additional Inherited Members

- Static Public Member Functions inherited from CLayoutGroup
static void PropagateRelatedSelection (bool isSelected, CSeqGlyph *pGlyph, CSeqGlyph *pGlyphFrom=NULL)
 set "RelatedGlyphSelected" in CLayoutGroup-based glyph hierarchies everywhere in the hierarchy containing the given glyph More...
 
- Static Public Member Functions inherited from CSeqGlyph
static bool PointInRect (const TModelPoint &p, const TModelRect &rc)
 
static bool PointInRect (TModelUnit x, TModelUnit y, const TModelRect &rc)
 
- 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)
 
- 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 Attributes inherited from CSeqGlyph
CSeqGlyphm_Parent
 parent/child relationships for this feature More...
 
CRenderingContextm_Context
 the rendering context More...
 
unique_ptr< CRgbaColorm_HighlightsColor
 Highlight color. More...
 
ENeighbours m_Neighbours
 Indicates whether the glyph has neighbours. More...
 

Detailed Description

CGeneGroup is a subclass of CLayoutGroup contains gene, RNA, cds, and Exon features.

CGeneGroup is able to deal gene model rendering when merging RNA-CDS pair, merging all RNAs and CDSs, and hiding gene features.

Definition at line 47 of file gene_model_group.hpp.

Member Enumeration Documentation

◆ EGene

Enumerator
eGene_Shown 

show gene bar

eGene_ShowLabelOnly 

hide gene bar, but show label with bar space

eGene_Hidden 

hide gene bar and gene label completely

Definition at line 52 of file gene_model_group.hpp.

Constructor & Destructor Documentation

◆ CGeneGroup()

CGeneGroup::CGeneGroup ( )
inline

Definition at line 58 of file gene_model_group.hpp.

◆ ~CGeneGroup()

virtual CGeneGroup::~CGeneGroup ( void  )
inlinevirtual

Definition at line 59 of file gene_model_group.hpp.

Member Function Documentation

◆ Accept()

bool CGeneGroup::Accept ( IGlyphVisitor visitor)
virtual

Interface for accepting an IGlyphVisitor.

The visitor will be passed to its child glyphs for composite glyph.

Returns
true if continue the traversal and false, otherwise.

Reimplemented from CLayoutGroup.

Definition at line 107 of file gene_model_group.cpp.

References CLayoutGroup::SetChildren(), and IGlyphVisitor::Visit().

◆ GetHTMLActiveAreas()

void CGeneGroup::GetHTMLActiveAreas ( TAreaVector ) const
virtual

◆ GetIntervals()

const CGeneGroup::TIntervals & CGeneGroup::GetIntervals ( ) const
virtual

access sub-intervals (if any).

Implements IObjectBasedGlyph.

Definition at line 191 of file gene_model_group.cpp.

References CFeatGlyph::GetIntervals(), and x_GetFirstFeat().

◆ GetLocation()

const objects::CSeq_loc & CGeneGroup::GetLocation ( ) const
virtual

access the position of this object.

Implements IObjectBasedGlyph.

Definition at line 176 of file gene_model_group.cpp.

References CFeatGlyph::GetLocation(), and x_GetFirstFeat().

Referenced by GetRange().

◆ GetObject()

CConstRef< CObject > CGeneGroup::GetObject ( TSeqPos  pos) const
virtual

access our core component - we wrap an object(s) of some sort.

This returns the object at a given sequence position; this is useful if the layout object wraps more than one object

Implements IObjectBasedGlyph.

Definition at line 153 of file gene_model_group.cpp.

References CFeatGlyph::GetObject(), and x_GetFirstFeat().

◆ GetObjects()

void CGeneGroup::GetObjects ( vector< CConstRef< CObject > > &  objs) const
virtual

retrieve CObjects corresponding to this CSeqGlyph.

Implements IObjectBasedGlyph.

Definition at line 159 of file gene_model_group.cpp.

References CFeatGlyph::GetObjects(), and x_GetFirstFeat().

◆ GetRange()

TSeqRange CGeneGroup::GetRange ( void  ) const
virtual

Get gene feature range instead.

Reimplemented from CSeqGlyph.

Definition at line 101 of file gene_model_group.cpp.

References GetLocation().

Referenced by x_Draw().

◆ GetSignature()

string CGeneGroup::GetSignature ( ) const
virtual

return signature for this glyph.

Implements IObjectBasedGlyph.

Definition at line 184 of file gene_model_group.cpp.

References CFeatGlyph::GetSignature(), and x_GetFirstFeat().

◆ HasObject()

bool CGeneGroup::HasObject ( CConstRef< CObject obj) const
virtual

check if the wrapped object(s) is the one.

Implements IObjectBasedGlyph.

Definition at line 165 of file gene_model_group.cpp.

References CFeatGlyph::HasObject(), and x_GetFirstFeat().

◆ HideGeneAndLabel()

void CGeneGroup::HideGeneAndLabel ( )
inline

CGeneGroup inline methods.

Definition at line 234 of file gene_model_group.hpp.

References eGene_Hidden, and m_ShowGene.

◆ SetShowGene()

void CGeneGroup::SetShowGene ( bool  flag)

◆ Update()

void CGeneGroup::Update ( bool  layout_only)
virtual

◆ x_Draw()

void CGeneGroup::x_Draw ( ) const
protectedvirtual

◆ x_GetFirstFeat()

const CFeatGlyph * CGeneGroup::x_GetFirstFeat ( ) const
private

◆ x_GetLabelHeight()

TModelUnit CGeneGroup::x_GetLabelHeight ( ) const
protected

Returns the height of the label with margin included.

Definition at line 336 of file gene_model_group.cpp.

References _ASSERT, CLayoutGroup::GetChildren(), CFeatGlyph::GetConfig(), GetGl(), CFeatureParams::m_LabelFont, and IRender::TextHeight().

Referenced by x_Draw().

◆ x_ShowGeneLabel()

bool CGeneGroup::x_ShowGeneLabel ( ) const
protected

Member Data Documentation

◆ m_ShowGene

EGene CGeneGroup::m_ShowGene
private

The documentation for this class was generated from the following files:
Modified on Sun Jul 14 04:56:02 2024 by modify_doxy.py rev. 669887