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< CHTMLActiveArea >	TAreaVector

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< Uint8 >	TCounter
	Counter type is CAtomiCounter. More...

typedef Uint8	TCount
	Alias for value type of counter. More...

Public Types inherited from IObjectBasedGlyph
typedef vector< TSeqRange >	TIntervals

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< CObject >	GetObject (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 TIntervals &	GetIntervals () 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 TObjectList &	GetChildren () const
	CLayoutGroup inline methods. More...

TObjectList &	GetChildren ()

size_t	GetChildrenNum () const
	Get total number of children. More...

CConstRef< CSeqGlyph >	GetChild (int idx) const
	Get the layout object at index 'idx'. More...

CRef< CSeqGlyph >	GetChild (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)

TObjectList &	SetChildren ()

void	Clear ()

virtual CRef< CSeqGlyph >	HitTest (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 CRenderingContext *	GetRenderingContext () 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

CRgbaColor *	GetHighlightsColor () 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 TModelPoint &	GetPos () const

void	GetPosInWorld (TModelPoint &pos) const
	Get top left position in world coordinate. More...

const CSeqGlyph *	GetParent (void) const

CSeqGlyph *	GetParent (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)

CSeqGlyph *	SetParent (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...

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 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 CFeatGlyph *	x_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
CSeqGlyph *	m_Parent
	parent/child relationships for this feature More...

CRenderingContext *	m_Context
	the rendering context More...

unique_ptr< CRgbaColor >	m_HighlightsColor
	Highlight color. More...

ENeighbours	m_Neighbours
	Indicates whether the glyph has neighbours. More...