Search Toolkit Book for CLinkedFeatsGroup

CLinkedFeatsGroup is a container class contains related features. More...

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

Inheritance diagram for CLinkedFeatsGroup:

Collaboration diagram for CLinkedFeatsGroup:

Public Types
enum	FLabelType { fLabel_ParentLabel = 1 << 0 , fLabel_FeatNum = 1 << 1 , fLabel_Both = fLabel_ParentLabel \| fLabel_FeatNum }

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
	CLinkedFeatsGroup ()
	CLinkedFeatsGroup implementations. More...

virtual	~CLinkedFeatsGroup (void)

void	SetConfig (const CFeatureParams *conf)

CLayoutGroup &	SetGroup ()

void	SetParentFeat (const CFeatGlyph *feat)

CConstRef< CFeatGlyph >	GetParentFeat () const

void	SetLabelType (FLabelType type)

void	SetFirstIsParent ()

bool	isRmtBased () const

void	SetShowLabel (bool show_label=true)

CSeqGlyph interface implementation
virtual void	Update (bool layout_only)
	Update content and layout including the bounding box. More...

virtual CRef< CSeqGlyph >	HitTest (const TModelPoint &p)
	Hit testing. More...

virtual bool	Intersects (const TModelRect &rect, TConstObjects &objs) const
	Intersect testing. More...

virtual bool	NeedTooltip (const TModelPoint &p, ITooltipFormatter &tt, string &t_title) const
	Check if need to show tooltip. More...

virtual void	GetTooltip (const TModelPoint &p, ITooltipFormatter &tt, string &t_title) const
	Get the tooltip if available. More...

virtual void	GetHTMLActiveAreas (TAreaVector *p_areas) const
	Get html active areas. More...

virtual TSeqRange	GetRange (void) const
	get the total range of this object. More...

virtual bool	SetSelected (bool f)
	Select or deselect this glyph. More...

virtual bool	Accept (IGlyphVisitor *visitor)
	Interface for accepting an IGlyphVisitor. More...

virtual bool	IsClickable () const
	Query if this glyph is clickable. 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...

delegate methods of CLayoutGroup
const ILayoutPolicy::TObjectList &	GetChildren () const
	CLinkedFeatsGroup inline methods. More...

ILayoutPolicy::TObjectList &	SetChildren ()

void	PushBack (CSeqGlyph *obj)

void	SetLayoutPolicy (ILayoutPolicy *policy)

Public Member Functions inherited from CSeqGlyph
	CSeqGlyph ()

virtual	~CSeqGlyph ()

virtual bool	HitTestHor (TSeqPos x, const CObject *obj)

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	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
CSeqGlyph virtual methods.
virtual void	x_Draw () const
	The default renderer for this layout object. More...

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 Types
typedef vector< int >	TCounts

Private Member Functions
bool	x_ShowLabel () const
	Check if need to show label. More...

bool	x_LabelFirst () const
	check to see if label needs to be drawn before (above) feature bar. More...

void	x_DrawLabels (TModelUnit &base, bool draw_left=true, bool draw_right=true) const
	draw the labels for merged features. More...

void	x_DrawChildrenOnParent (TModelUnit &base) const
	draw the merged feature bar with children on top of parent. More...

void	x_DrawFeatureBar (TModelUnit &base) const
	draw the merged feature bar. More...

void	x_CalcIntervals ()
	calculate the merged feature bar intervals and overlapping counts. More...

void	x_GetUniqueLabel (string &label) const
	utility method for generating a unique label for the merged bar. More...

const CFeatGlyph *	x_GetFirstFeat () const
	get the first feature glyph in the group. More...

const CFeatGlyph *	x_GetLastFeat () const
	get the last feature glyph in the group. More...

TModelUnit	x_GetLabelHeight () const
	Returns the height of the label with margin included. More...

void	x_AddFeatHTMLActiveArea (TAreaVector p_areas, const CFeatGlyph feat, unsigned merged_feats_count=0) const

bool	x_AreAllFeaturesOnSameStrand () const

Private Attributes
CRef< objects::CSeq_loc >	m_Location
	just for satisfy IObjectBasedGlyph interface. More...

CLayoutGroup	m_Group

CConstRef< CFeatGlyph >	m_ParentFeat

FLabelType	m_LabelType

CConstRef< CFeatureParams >	m_Config
	settings for rendering merged feature bar. More...

TIntervals	m_Intervals

TCounts	m_IntCounts
	Shall have the same size as m_Intervals. More...

bool	m_FirstIsParent
	The first feature is the parent feature. More...

bool	m_ShowLabel = true

Additional Inherited Members
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...

Detailed Description

CLinkedFeatsGroup is a container class contains related features.

CLinkedFeatsGroup can merge all the features it contains and show the merged features into on single bar consisting of a set of segments. Each segment may have a different intensity color to indicate the number of features overlaping within that region.

Definition at line 109 of file gene_model_group.hpp.

Member Typedef Documentation

◆ TCounts

typedef vector<int> CLinkedFeatsGroup::TCounts

private

Definition at line 213 of file gene_model_group.hpp.

Member Enumeration Documentation

◆ FLabelType

enum CLinkedFeatsGroup::FLabelType

Enumerator
fLabel_ParentLabel
fLabel_FeatNum
fLabel_Both

Definition at line 117 of file gene_model_group.hpp.

Constructor & Destructor Documentation

◆ CLinkedFeatsGroup()

CLinkedFeatsGroup::CLinkedFeatsGroup ( )

CLinkedFeatsGroup implementations.

Definition at line 359 of file gene_model_group.cpp.

References m_Group, m_Location, CRef< C, Locker >::Reset(), and CSeqGlyph::SetParent().

◆ ~CLinkedFeatsGroup()

virtual CLinkedFeatsGroup::~CLinkedFeatsGroup ( void )

inlinevirtual

Definition at line 115 of file gene_model_group.hpp.

Member Function Documentation

◆ Accept()

bool CLinkedFeatsGroup::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 CSeqGlyph.

Definition at line 552 of file gene_model_group.cpp.

References IGlyphVisitor::Visit().

◆ GetChildren()

const ILayoutPolicy::TObjectList & CLinkedFeatsGroup::GetChildren ( void ) const

inline

CLinkedFeatsGroup inline methods.

Definition at line 244 of file gene_model_group.hpp.

References CLayoutGroup::GetChildren(), and m_Group.

Referenced by GetHTMLActiveAreas(), GetObjects(), GetTooltip(), HasObject(), CGeneGroup::SetShowGene(), x_AreAllFeaturesOnSameStrand(), x_CalcIntervals(), x_Draw(), x_DrawChildrenOnParent(), x_DrawFeatureBar(), x_DrawLabels(), x_GetFirstFeat(), x_GetLastFeat(), and x_UpdateBoundingBox().

◆ GetHTMLActiveAreas()

void CLinkedFeatsGroup::GetHTMLActiveAreas ( TAreaVector * ) const

virtual

Get html active areas.

This function is for CGI mode only. By default, it does nothing.

Reimplemented from CSeqGlyph.

Definition at line 475 of file gene_model_group.cpp.

References bound(), GetChildren(), CLayoutGroup::GetHTMLActiveAreas(), if(), CSeqGlyph::IsHighlighted(), CSeqGlyph::IsSelected(), ITERATE, CFeatureParams::m_BarHeight, m_Config, m_FirstIsParent, m_Group, m_ParentFeat, ncbi::grid::netcache::search::fields::size, x_AddFeatHTMLActiveArea(), x_GetFirstFeat(), x_GetLabelHeight(), x_GetLastFeat(), and x_LabelFirst().

◆ GetIntervals()

const CLinkedFeatsGroup::TIntervals & CLinkedFeatsGroup::GetIntervals ( ) const

virtual

access sub-intervals (if any).

Implements IObjectBasedGlyph.

Definition at line 614 of file gene_model_group.cpp.

References m_Intervals.

◆ GetLocation()

const objects::CSeq_loc & CLinkedFeatsGroup::GetLocation ( ) const

virtual

access the position of this object.

Implements IObjectBasedGlyph.

Definition at line 565 of file gene_model_group.cpp.

References m_Location.

Referenced by x_DrawLabels(), x_LabelFirst(), and x_UpdateBoundingBox().

◆ GetObject()

CConstRef< CObject > CLinkedFeatsGroup::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 571 of file gene_model_group.cpp.

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

◆ GetObjects()

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

virtual

retrieve CObjects corresponding to this CSeqGlyph.

Implements IObjectBasedGlyph.

Definition at line 579 of file gene_model_group.cpp.

References GetChildren(), CFeatGlyph::GetObjects(), ITERATE, and LOG_POST.

◆ GetParentFeat()

CConstRef< CFeatGlyph > CLinkedFeatsGroup::GetParentFeat ( ) const

inline

Definition at line 272 of file gene_model_group.hpp.

References m_ParentFeat.

◆ GetRange()

TSeqRange CLinkedFeatsGroup::GetRange ( void ) const

virtual

get the total range of this object.

CSeqGlyph inline methods.

Reimplemented from CSeqGlyph.

Definition at line 531 of file gene_model_group.cpp.

References ITERATE, m_Intervals, and compile_time_bits::range().

Referenced by x_Draw().

◆ GetSignature()

string CLinkedFeatsGroup::GetSignature ( ) const

virtual

return signature for this glyph.

Implements IObjectBasedGlyph.

Definition at line 607 of file gene_model_group.cpp.

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

◆ GetTooltip()

void CLinkedFeatsGroup::GetTooltip	(	const TModelPoint &	,
		ITooltipFormatter &	tt,
		string &	t_title
	)		const

virtual

Get the tooltip if available.

The x and y are in 'world' coord system which is the coord. system for the uppermost layout object.

Reimplemented from CSeqGlyph.

Definition at line 416 of file gene_model_group.cpp.

References CCreateParamsSeqFeatGroup::Add(), ITooltipFormatter::AddRow(), GetChildren(), CFeatGlyph::GetMappedFeature(), CMappedFeat::GetMappedFeature(), CFeatGlyph::GetMappingInfo(), CFeatGlyph::GetTooltip(), int, CSeqGlyph::IsSelected(), ITERATE, NStr::LongToString(), m_FirstIsParent, m_ParentFeat, rapidjson::value, CGlPoint< T >::X(), and x_GetFirstFeat().

Referenced by x_AddFeatHTMLActiveArea().

◆ HasObject()

bool CLinkedFeatsGroup::HasObject ( CConstRef< CObject > obj ) const

virtual

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

Implements IObjectBasedGlyph.

Definition at line 594 of file gene_model_group.cpp.

References GetChildren(), CFeatGlyph::HasObject(), and ITERATE.

◆ HitTest()

CRef< CSeqGlyph > CLinkedFeatsGroup::HitTest ( const TModelPoint & p )

virtual

Hit testing.

Test whether a given point in PARENT's COORD. SYSTEM falls inside this layout object. Recursive hit testing may happen if this layout object is a container of other layout objects.

Returns: the object that gets hit.

Reimplemented from CSeqGlyph.

Definition at line 380 of file gene_model_group.cpp.

References CLayoutGroup::HitTest(), CSeqGlyph::IsIn(), CSeqGlyph::IsSelected(), m_Group, CRef< C, Locker >::Reset(), and CSeqGlyph::x_Parent2Local().

◆ Intersects()

bool CLinkedFeatsGroup::Intersects	(	const TModelRect &	rect,
		TConstObjects &	objs
	)		const

virtual

Intersect testing.

Test weather a given rectangular area intersects with this layout object. Recursive intersect testing is necessary if the layout object is a container of other containers. All the intersected leaf objects will be added into objs. The rect is in parent's coord system.

Reimplemented from CSeqGlyph.

Definition at line 399 of file gene_model_group.cpp.

References CSeqGlyph::GetModelRect(), and CGlRect< T >::Intersects().

◆ IsClickable()

bool CLinkedFeatsGroup::IsClickable ( ) const

virtual

Query if this glyph is clickable.

Mainly for chaging mouse cursor for clickable glyph. By default, it returns false. If a glyph is clickable, but there is no need to change mouse cursor due to any other reason, such as there is already other visual hint, then don't need to override this function.

Reimplemented from CSeqGlyph.

Definition at line 559 of file gene_model_group.cpp.

◆ isRmtBased()

bool CLinkedFeatsGroup::isRmtBased ( ) const

Definition at line 460 of file gene_model_group.cpp.

References _ASSERT, CFeatGlyph::isRmtBased(), m_FirstIsParent, m_ParentFeat, and x_GetFirstFeat().

Referenced by x_AddFeatHTMLActiveArea().

◆ NeedTooltip()

bool CLinkedFeatsGroup::NeedTooltip	(	const TModelPoint &	,
		ITooltipFormatter &	,
		string &	t_title
	)		const

virtual

Check if need to show tooltip.

If the tooltip retrieval is trivial, the derived glyph may decide to fill out the tooltip (info object) in this call.

Reimplemented from CSeqGlyph.

Definition at line 410 of file gene_model_group.cpp.

◆ PushBack()

void CLinkedFeatsGroup::PushBack ( CSeqGlyph * obj )

inline

Definition at line 252 of file gene_model_group.hpp.

References m_Group, and CLayoutGroup::PushBack().

Referenced by CGeneModelFeatJob::x_CreateGeneModels(), and CFeatureTrack::x_ExtracGlyphs_Recursive().

◆ SetChildren()

ILayoutPolicy::TObjectList & CLinkedFeatsGroup::SetChildren ( void )

inline

Definition at line 248 of file gene_model_group.hpp.

References m_Group, and CLayoutGroup::SetChildren().

◆ SetConfig()

void CLinkedFeatsGroup::SetConfig ( const CFeatureParams * conf )

inline

Definition at line 260 of file gene_model_group.hpp.

References m_Config, and CConstRef< C, Locker >::Reset().

◆ SetFirstIsParent()

void CLinkedFeatsGroup::SetFirstIsParent ( )

inline

Definition at line 280 of file gene_model_group.hpp.

References m_FirstIsParent.

◆ SetGroup()

CLayoutGroup & CLinkedFeatsGroup::SetGroup ( void )

inline

Definition at line 264 of file gene_model_group.hpp.

References m_Group.

Referenced by CGeneModelFeatJob::x_CreateGeneModels().

◆ SetLabelType()

void CLinkedFeatsGroup::SetLabelType ( CLinkedFeatsGroup::FLabelType type )

inline

Definition at line 276 of file gene_model_group.hpp.

References m_LabelType, and type.

◆ SetLayoutPolicy()

void CLinkedFeatsGroup::SetLayoutPolicy ( ILayoutPolicy * policy )

inline

Definition at line 256 of file gene_model_group.hpp.

References m_Group, and CLayoutGroup::SetLayoutPolicy().

◆ SetParentFeat()

void CLinkedFeatsGroup::SetParentFeat ( const CFeatGlyph * feat )

inline

Definition at line 268 of file gene_model_group.hpp.

References m_ParentFeat, and CConstRef< C, Locker >::Reset().

◆ SetSelected()

bool CLinkedFeatsGroup::SetSelected ( bool flag )

virtual

Select or deselect this glyph.

By default, it only set/unset m_Selected flag. Some concrete glyphs may need to override this method to change other glyph properties and layout when selected or deselected, e.g. show additional features. returns true if a layout update (ePUA_CallLayoutChanged) is required after all selections are processed

Reimplemented from CSeqGlyph.

Definition at line 541 of file gene_model_group.cpp.

References f(), CSeqGlyph::IsSelected(), m_Group, CSeqGlyph::SetSelected(), CLayoutGroup::Update(), and CSeqGlyph::x_OnLayoutChanged().

◆ SetShowLabel()

void CLinkedFeatsGroup::SetShowLabel ( bool show_label = true )

inline

Definition at line 284 of file gene_model_group.hpp.

References m_ShowLabel.

◆ Update()

void CLinkedFeatsGroup::Update ( bool )

virtual

Update content and layout including the bounding box.

Parameters

layout_only if true only update the layout not the content. May need to update the layout only under certain situation, e.g. selection. The update is recursive if this is a container layout. By default, it updates the bounding box only.

Reimplemented from CSeqGlyph.

Definition at line 371 of file gene_model_group.cpp.

References CSeqGlyph::IsHighlighted(), CSeqGlyph::IsSelected(), m_Group, CLayoutGroup::Update(), and x_UpdateBoundingBox().

◆ x_AddFeatHTMLActiveArea()

void CLinkedFeatsGroup::x_AddFeatHTMLActiveArea	(	TAreaVector *	p_areas,
		const CFeatGlyph *	feat,
		unsigned	merged_feats_count = `0`
	)		const

private

◆ x_AreAllFeaturesOnSameStrand()

bool CLinkedFeatsGroup::x_AreAllFeaturesOnSameStrand ( ) const

private

Definition at line 1406 of file gene_model_group.cpp.

References _ASSERT, eNa_strand_minus, GetChildren(), CFeatGlyph::GetLocation(), and GetStrand().

Referenced by x_DrawChildrenOnParent().

◆ x_CalcIntervals()

void CLinkedFeatsGroup::x_CalcIntervals ( void )

private

calculate the merged feature bar intervals and overlapping counts.

Definition at line 1214 of file gene_model_group.cpp.

References _ASSERT, cnt, f(), GetChildren(), CFeatGlyph::GetIntervals(), ITERATE, m_IntCounts, m_Intervals, and t.

Referenced by x_UpdateBoundingBox().

◆ x_Draw()

void CLinkedFeatsGroup::x_Draw ( ) const

protectedvirtual

The default renderer for this layout object.

Implements CSeqGlyph.

Definition at line 620 of file gene_model_group.cpp.

References CSeqGlyph::Draw(), CRenderingContext::DrawSelection(), Empty(), CFeatureParams::ePos_Above, CFeatureParams::ePos_NoLabel, CFeatureParams::ePos_Side, CFeatureParams::GetBarHeight(), GetChildren(), CFeatGlyph::GetFeature(), CRange_Base::GetFrom(), GetGl(), CSeqGlyph::GetLeft(), CSeqGlyph::GetModelRect(), GetRange(), CRange_Base::GetTo(), CSeqGlyph::GetTop(), CRenderingContext::IntersectVisible(), CSeqUtils::IsException(), CSeqGlyph::IsHighlighted(), CSeqGlyph::IsSelected(), m_Config, CSeqGlyph::m_Context, m_FirstIsParent, m_Group, CFeatureParams::m_LabelPos, IRender::PopMatrix(), IRender::PushMatrix(), r(), IRender::Translatef(), x_DrawChildrenOnParent(), CSeqGlyph::x_DrawException(), x_DrawFeatureBar(), x_DrawLabels(), and x_LabelFirst().

◆ x_DrawChildrenOnParent()

void CLinkedFeatsGroup::x_DrawChildrenOnParent ( TModelUnit & base ) const

private

draw the merged feature bar with children on top of parent.

Definition at line 956 of file gene_model_group.cpp.

References _ASSERT, CRgbaColor::ContrastingColor(), CRenderingContext::Draw3DQuad(), CRenderingContext::DrawStrandIndicators(), eNa_strand_both, eNa_strand_both_rev, eNa_strand_minus, f(), GetChildren(), CFeatGlyph::GetConfig(), CFeatGlyph::GetCustomColor(), CRange_Base::GetFrom(), COpenRange< Position >::GetLength(), CFeatGlyph::GetLocation(), CFeatGlyph::GetRange(), GetStrand(), CRange_Base::GetTo(), ITERATE, CFeatureParams::m_BarHeight, m_Config, CSeqGlyph::m_Context, CFeatureParams::m_fgColor, CFeatureParams::m_ShowStrandIndicator, CRenderingContext::ScreenToSeq(), CRgbaColor::SetAlpha(), CRgbaColor::SetBlue(), CRgbaColor::SetGreen(), t, x_AreAllFeaturesOnSameStrand(), and x_GetFirstFeat().

Referenced by x_Draw().

◆ x_DrawFeatureBar()

void CLinkedFeatsGroup::x_DrawFeatureBar ( TModelUnit & base ) const

private

draw the merged feature bar.

Definition at line 1020 of file gene_model_group.cpp.

References color, IRender::ColorC(), CRgbaColor::ContrastingColor(), IRender::Disable(), CRenderingContext::Draw3DQuad(), CRenderingContext::DrawLine(), CRenderingContext::DrawQuad(), CRenderingContext::DrawStrandIndicators(), CFeatureParams::eBox, CFeatureParams::eCantedLine, CFeatureParams::eFilledBox, CFeatureParams::eLine_DashDotted, CFeatureParams::eLine_Dashed, CFeatureParams::eLine_Dotted, CFeatureParams::eLine_ShortDashed, CFeatureParams::eLine_Solid, eNa_strand_both, eNa_strand_both_rev, eNa_strand_minus, IRender::Enable(), CFeatureParams::eStraightLine, f(), fabs, GetChildren(), CFeatGlyph::GetConfig(), CFeatGlyph::GetCustomColor(), CFeatGlyph::GetCustomColorIdx(), CFeatGlyph::GetFeature(), CRange_Base::GetFrom(), GetGl(), CFeatGlyph::GetLocation(), GetStrand(), CRange_Base::GetTo(), i, CRgbaColor::Interpolate(), CRenderingContext::IntersectVisible(), CFeatGlyph::IsDbVar(), ITERATE, CRgbaColor::Lighten(), IRender::LineStipple(), IRender::LineWidth(), CFeatureParams::m_BarHeight, m_Config, CFeatureParams::m_Connections, CSeqGlyph::m_Context, CFeatureParams::m_fgColor, m_IntCounts, m_Intervals, CFeatureParams::m_LineStyle, CFeatureParams::m_LineWidth, CFeatureParams::m_ShowStrandIndicator, COpenRange< Position >::NotEmpty(), compile_time_bits::range(), CRenderingContext::ScreenToSeq(), CRenderingContext::SeqToScreen(), t, and x_GetFirstFeat().

Referenced by x_Draw().

◆ x_DrawHighlight()

virtual void CLinkedFeatsGroup::x_DrawHighlight ( ) const

inlineprotectedvirtual

override x_DrawHighlight() to do nothing.

Reimplemented from CSeqGlyph.

Definition at line 174 of file gene_model_group.hpp.

◆ x_DrawLabels()

void CLinkedFeatsGroup::x_DrawLabels	(	TModelUnit &	base,
		bool	draw_left = `true`,
		bool	draw_right = `true`
	)		const

private

draw the labels for merged features.

Definition at line 795 of file gene_model_group.cpp.

Referenced by x_Draw().

◆ x_GetFirstFeat()

const CFeatGlyph * CLinkedFeatsGroup::x_GetFirstFeat ( ) const

private

get the first feature glyph in the group.

Definition at line 1341 of file gene_model_group.cpp.

References _ASSERT, GetChildren(), ITERATE, and NULL.

Referenced by GetHTMLActiveAreas(), GetObject(), GetTooltip(), isRmtBased(), x_DrawChildrenOnParent(), x_DrawFeatureBar(), x_DrawLabels(), x_GetUniqueLabel(), x_ShowLabel(), and x_UpdateBoundingBox().

◆ x_GetLabelHeight()

TModelUnit CLinkedFeatsGroup::x_GetLabelHeight ( ) const

private

Returns the height of the label with margin included.

Definition at line 1366 of file gene_model_group.cpp.

References GetGl(), m_Config, CFeatureParams::m_LabelFont, and IRender::TextHeight().

Referenced by GetHTMLActiveAreas(), x_DrawLabels(), and x_UpdateBoundingBox().

◆ x_GetLastFeat()

const CFeatGlyph * CLinkedFeatsGroup::x_GetLastFeat ( ) const

private

get the last feature glyph in the group.

Definition at line 1353 of file gene_model_group.cpp.

References _ASSERT, GetChildren(), and NULL.

Referenced by GetHTMLActiveAreas(), and GetSignature().

◆ x_GetUniqueLabel()

void CLinkedFeatsGroup::x_GetUniqueLabel ( string & label ) const

private

utility method for generating a unique label for the merged bar.

Definition at line 1315 of file gene_model_group.cpp.

References CLabel::eContent, fLabel_FeatNum, fLabel_ParentLabel, CLayoutGroup::GetChildrenNum(), CFeatGlyph::GetLabel(), CSeqGlyph::IsHighlighted(), CSeqGlyph::IsSelected(), kEmptyStr, label, m_FirstIsParent, m_Group, m_LabelType, m_ParentFeat, NStr::NumericToString(), NStr::SizetToString(), and x_GetFirstFeat().

Referenced by x_DrawLabels(), and x_UpdateBoundingBox().

◆ x_LabelFirst()

bool CLinkedFeatsGroup::x_LabelFirst ( ) const

private

check to see if label needs to be drawn before (above) feature bar.

Definition at line 774 of file gene_model_group.cpp.

References eNa_strand_minus, CFeatureParams::ePos_Above, CFeatureParams::ePos_Side, first(), CSeqGlyph::GetLeft(), GetLocation(), CSeqGlyph::GetRight(), CRenderingContext::GetSeqDS(), CSGSequenceDS::GetSequenceLength(), GetStrand(), m_Config, CSeqGlyph::m_Context, and CFeatureParams::m_LabelPos.

Referenced by GetHTMLActiveAreas(), x_Draw(), x_DrawLabels(), and x_UpdateBoundingBox().

◆ x_ShowLabel()

bool CLinkedFeatsGroup::x_ShowLabel ( ) const

private

Check if need to show label.

Definition at line 768 of file gene_model_group.cpp.

References CFeatureParams::ePos_NoLabel, CFeatGlyph::IsLabelHided(), m_Config, CFeatureParams::m_LabelPos, m_ShowLabel, and x_GetFirstFeat().

Referenced by x_DrawLabels(), and x_UpdateBoundingBox().

◆ x_UpdateBoundingBox()

void CLinkedFeatsGroup::x_UpdateBoundingBox ( )

protectedvirtual

Update the bounding box assuming children's sizes are fixed if any.

Implements CSeqGlyph.

Definition at line 687 of file gene_model_group.cpp.

References CLabel::eContent, eNa_strand_minus, CFeatureParams::ePos_Side, fLabel_FeatNum, CLayoutGroup::GetChild(), GetChildren(), GetGl(), CSeqGlyph::GetHeight(), CFeatGlyph::GetLabel(), CSeqGlyph::GetLeft(), GetLocation(), CRenderingContext::GetMaxLabelWidth(), CRef< C, Locker >::GetPointer(), CSeqGlyph::GetRight(), GetStrand(), CSeqGlyph::GetWidth(), CRenderingContext::IntersectVisible(), CSeqGlyph::IsHighlighted(), CSeqGlyph::IsSelected(), kLabelSpace, kVertSpace, label, CFeatureParams::m_BarHeight, m_Config, CSeqGlyph::m_Context, m_Group, m_Intervals, CFeatureParams::m_LabelFont, CFeatureParams::m_LabelPos, m_LabelType, max(), min(), compile_time_bits::range(), CRenderingContext::ScreenToSeq(), CSeqGlyph::SetHeight(), CSeqGlyph::SetLeft(), CSeqGlyph::SetTop(), CSeqGlyph::SetWidth(), IRender::TextHeight(), IRender::TextWidth(), CRenderingContext::WillLabelFit(), x_CalcIntervals(), x_GetFirstFeat(), x_GetLabelHeight(), x_GetUniqueLabel(), x_LabelFirst(), and x_ShowLabel().

Referenced by Update().

Member Data Documentation

◆ m_Config

CConstRef<CFeatureParams> CLinkedFeatsGroup::m_Config

private

settings for rendering merged feature bar.

Definition at line 222 of file gene_model_group.hpp.

Referenced by GetHTMLActiveAreas(), SetConfig(), x_Draw(), x_DrawChildrenOnParent(), x_DrawFeatureBar(), x_DrawLabels(), x_GetLabelHeight(), x_LabelFirst(), x_ShowLabel(), and x_UpdateBoundingBox().

◆ m_FirstIsParent

bool CLinkedFeatsGroup::m_FirstIsParent

private

The first feature is the parent feature.

Definition at line 225 of file gene_model_group.hpp.

Referenced by GetHTMLActiveAreas(), GetTooltip(), isRmtBased(), SetFirstIsParent(), x_Draw(), x_DrawLabels(), and x_GetUniqueLabel().

◆ m_Group

CLayoutGroup CLinkedFeatsGroup::m_Group

private

Definition at line 217 of file gene_model_group.hpp.

Referenced by CLinkedFeatsGroup(), GetChildren(), GetHTMLActiveAreas(), HitTest(), PushBack(), SetChildren(), SetGroup(), SetLayoutPolicy(), SetSelected(), Update(), x_Draw(), x_DrawLabels(), x_GetUniqueLabel(), and x_UpdateBoundingBox().

◆ m_IntCounts

TCounts CLinkedFeatsGroup::m_IntCounts

private

Shall have the same size as m_Intervals.

Definition at line 224 of file gene_model_group.hpp.

Referenced by x_CalcIntervals(), and x_DrawFeatureBar().

◆ m_Intervals

TIntervals CLinkedFeatsGroup::m_Intervals

private

Definition at line 223 of file gene_model_group.hpp.

Referenced by GetIntervals(), GetRange(), x_CalcIntervals(), x_DrawFeatureBar(), x_DrawLabels(), and x_UpdateBoundingBox().

◆ m_LabelType

FLabelType CLinkedFeatsGroup::m_LabelType

private

Definition at line 219 of file gene_model_group.hpp.

Referenced by SetLabelType(), x_DrawLabels(), x_GetUniqueLabel(), and x_UpdateBoundingBox().

◆ m_Location

CRef<objects::CSeq_loc> CLinkedFeatsGroup::m_Location

private

just for satisfy IObjectBasedGlyph interface.

Definition at line 216 of file gene_model_group.hpp.

Referenced by CLinkedFeatsGroup(), and GetLocation().

◆ m_ParentFeat

CConstRef<CFeatGlyph> CLinkedFeatsGroup::m_ParentFeat

private

Definition at line 218 of file gene_model_group.hpp.

Referenced by GetHTMLActiveAreas(), GetParentFeat(), GetTooltip(), isRmtBased(), SetParentFeat(), x_DrawLabels(), and x_GetUniqueLabel().

◆ m_ShowLabel

bool CLinkedFeatsGroup::m_ShowLabel = true

private

Definition at line 226 of file gene_model_group.hpp.

Referenced by SetShowLabel(), and x_ShowLabel().

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

include/gui/widgets/seq_graphic/gene_model_group.hpp
src/gui/widgets/seq_graphic/gene_model_group.cpp

Public Types

Public Member Functions

Protected Member Functions

Private Types

Private Member Functions

Private Attributes

Additional Inherited Members

Detailed Description

Member Typedef Documentation

◆ TCounts

Member Enumeration Documentation

◆ FLabelType

Constructor & Destructor Documentation

◆ CLinkedFeatsGroup()

◆ ~CLinkedFeatsGroup()

Member Function Documentation

◆ Accept()

◆ GetChildren()

◆ GetHTMLActiveAreas()

◆ GetIntervals()

◆ GetLocation()

◆ GetObject()

◆ GetObjects()

◆ GetParentFeat()

◆ GetRange()

◆ GetSignature()

◆ GetTooltip()

◆ HasObject()

◆ HitTest()

◆ Intersects()

◆ IsClickable()

◆ isRmtBased()

◆ NeedTooltip()

◆ PushBack()

◆ SetChildren()

◆ SetConfig()

◆ SetFirstIsParent()

◆ SetGroup()

◆ SetLabelType()

◆ SetLayoutPolicy()

◆ SetParentFeat()

◆ SetSelected()

◆ SetShowLabel()

◆ Update()

◆ x_AddFeatHTMLActiveArea()

◆ x_AreAllFeaturesOnSameStrand()

◆ x_CalcIntervals()

◆ x_Draw()

◆ x_DrawChildrenOnParent()

◆ x_DrawFeatureBar()

◆ x_DrawHighlight()

◆ x_DrawLabels()

◆ x_GetFirstFeat()

◆ x_GetLabelHeight()

◆ x_GetLastFeat()

◆ x_GetUniqueLabel()

◆ x_LabelFirst()

◆ x_ShowLabel()

◆ x_UpdateBoundingBox()

Member Data Documentation

◆ m_Config

◆ m_FirstIsParent

◆ m_Group

◆ m_IntCounts

◆ m_Intervals

◆ m_LabelType

◆ m_Location

◆ m_ParentFeat

◆ m_ShowLabel