class CSeqGlyph defines an interface that wraps a rectilinear abstract object. More...

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

Inheritance diagram for CSeqGlyph:

Collaboration diagram for CSeqGlyph:

Classes
class	IGlyphRenderer
	Layout renderer interface. More...

Public Types
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 Member Functions
	CSeqGlyph ()

virtual	~CSeqGlyph ()

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...

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

virtual void	Update (bool)
	Update content and layout including the bounding box. More...

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

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

Mouse event handlers
Each layout object may have customized handlers on the following mouse events. The x and y are in 'world' coord system which is the coord. system for the uppermost layout object. Return true if event is consumed and false if not
virtual bool	OnLeftDown (const TModelPoint &)

virtual bool	OnLeftUp (const TModelPoint &)

virtual bool	OnLeftDblClick (const TModelPoint &)

virtual bool	OnContextMenu (wxContextMenuEvent &event)

Accessors
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

Mutators
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...

Static Public Member Functions
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)

Protected Member Functions
virtual void	x_Draw () const =0
	The default renderer for this layout object. More...

virtual void	x_UpdateBoundingBox ()=0
	Update the bounding box assuming children's sizes are fixed if any. More...

virtual void	x_DrawHighlight () const

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...

Protected Attributes
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...

Private Attributes
TModelUnit	m_Height
	object height More...

TModelUnit	m_Width
	object width More...

TModelPoint	m_Pos
	upper left corner position in parent coord More...

CIRef< IGlyphRenderer >	m_Renderer
	user-defined renderer More...

bool	m_Selected

bool	m_Highlighted

size_t	m_Tearline

size_t	m_RowNumber

bool	m_Visible

int	m_Level
	shows how deep is the glyph in an hierarchy (0 being closer to root, -1 undefined) More...

string	m_sTearlineText

Additional Inherited Members
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...

Detailed Description

class CSeqGlyph defines an interface that wraps a rectilinear abstract object.

CSeqGlyph defines how an axis-aligned rectilinear object appears to a layout algorithm. The basic concepts supported include: – querying rectilnear position or interval as a total range – functors for sorting – Draw() for rendering the object

Comments on the coordinate system for a layout object: 1. For most of the layout objects, the x coordinate (in horizontal mode) is predetermined and it is in the top sequence coordinate. So for a given layout object, we define the x origin of the local coord. system the same as the x origin of the 'world' coordinate system. 2. And y origin of the local coordinate will always be at the upper left corner (in horizontal mode) of the layout object. 3. From a developer's perspective, one can assume the sequence is in horizontal mode with no flipping strand.

Definition at line 81 of file seq_glyph.hpp.

Member Typedef Documentation

◆ TAreaVector

typedef vector<CHTMLActiveArea> CSeqGlyph::TAreaVector

Definition at line 84 of file seq_glyph.hpp.

◆ TConstObjects

typedef list< CConstRef<CSeqGlyph> > CSeqGlyph::TConstObjects

Definition at line 86 of file seq_glyph.hpp.

◆ TObjects

typedef list< CRef<CSeqGlyph> > CSeqGlyph::TObjects

Definition at line 85 of file seq_glyph.hpp.

Member Enumeration Documentation

◆ ENeighbours

enum CSeqGlyph::ENeighbours

Enumerator
eNghbrs_None
eNghbrs_Left
eNghbrs_Right
eNghbrs_Both

Definition at line 95 of file seq_glyph.hpp.

Constructor & Destructor Documentation

◆ CSeqGlyph()

CSeqGlyph::CSeqGlyph ( )

Definition at line 46 of file seq_glyph.cpp.

◆ ~CSeqGlyph()

virtual CSeqGlyph::~CSeqGlyph ( )

inlinevirtual

Definition at line 104 of file seq_glyph.hpp.

Member Function Documentation

◆ Accept()

bool CSeqGlyph::Accept ( IGlyphVisitor * visitor )

inlinevirtual

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 in CLayoutGroup, CGlyphContainer, CLinkedFeatsGroup, and CGeneGroup.

Definition at line 519 of file seq_glyph.hpp.

References IGlyphVisitor::Visit().

Referenced by CSelectionVisitor::GetSelectedLayoutObjects(), CSelectionVisitor::ResetObjectSelection(), CGlyphSearchVisitor::Search(), and CSelectionVisitor::UpdateSelection().

◆ Draw()

void CSeqGlyph::Draw ( void ) const

render the layout.

Definition at line 92 of file seq_glyph.cpp.

References IsHighlighted(), m_Renderer, x_Draw(), and x_DrawHighlight().

Referenced by CFeaturePanel::x_Draw(), CLinkedFeatsGroup::x_Draw(), CSeqGraphicRenderer::x_Draw(), CHistogramGlyph::x_DrawHeatMap(), CSeqGraphicRenderer::x_DrawVectorGraphics(), CGlyphContainer::x_RenderContent(), CGraphOverlay::x_RenderContent(), CSequenceTrack::x_RenderContent(), and CAlnVecRow::x_RenderTracks().

◆ GetBottom()

TModelUnit CSeqGlyph::GetBottom ( ) const

inlinevirtual

Definition at line 607 of file seq_glyph.hpp.

References m_Height, m_Pos, and CGlPoint< T >::Y().

Referenced by IsIn(), CAlignGlyph::x_Draw(), CClonePlacementGlyph::x_Draw(), CCommentGlyph::x_Draw(), CLegendItemGlyph::x_Draw(), CSegmentGlyph::x_Draw(), CTranslationGlyph::x_Draw(), CAlnStatGlyph::x_DrawBarGraph(), CAlnStatGlyph::x_DrawDensityTable(), x_DrawException(), CFeaturePanel::x_DrawHairLine(), CAlignGlyph::x_DrawPWAlign(), and CFeaturePanel::x_RenderFeatureGrid().

◆ GetFadeFactor()

float CSeqGlyph::GetFadeFactor ( ) const

inline

Definition at line 742 of file seq_glyph.hpp.

References GetRowNum(), GetTearline(), kFadeCount, and max().

Referenced by CAlignGlyph::ApplyFading(), and CMatePairGlyph::x_Draw().

◆ GetHeight()

TModelUnit CSeqGlyph::GetHeight ( void ) const

inlinevirtual

Definition at line 587 of file seq_glyph.hpp.

References m_Height.

◆ GetHighlightsColor()

CRgbaColor * CSeqGlyph::GetHighlightsColor ( ) const

inline

Definition at line 581 of file seq_glyph.hpp.

References m_HighlightsColor.

◆ GetHTMLActiveAreas()

virtual void CSeqGlyph::GetHTMLActiveAreas ( TAreaVector * ) const

inlinevirtual

Get html active areas.

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

Reimplemented in CLegendItemGlyph, CGeneModelTrack, CAlignmentTrack, CVcfGlyph, CTranslationGlyph, CTrackContainer, CTraceGraphTrack, CTraceGlyph, CSegmentGlyph, CRsitesGlyph, CNamedGroup, CMatePairGlyph, CLayoutGroup, CIntronTrack, CHistogramGlyph, CGraphTrack, CGraphOverlay, CGlyphContainer, CLinkedFeatsGroup, CGeneGroup, CFeatGlyph, CClonePlacementGlyph, CAlignGlyph, CAlnStatGlyph, CScatterPlotGlyph, CGeneMarkerGlyph, CBinsTrack, and CBinsGlyph.

Definition at line 148 of file seq_glyph.hpp.

◆ GetLeft()

TModelUnit CSeqGlyph::GetLeft ( ) const

inlinevirtual

Definition at line 595 of file seq_glyph.hpp.

References m_Pos, and CGlPoint< T >::X().

◆ GetLevel()

int CSeqGlyph::GetLevel ( ) const

inline

Definition at line 286 of file seq_glyph.hpp.

References m_Level.

Referenced by CFeatGlyph::GetLabel(), CLayoutGroup::PropagateRelatedSelection(), CGeneGroup::x_Draw(), CLayoutGroup::x_Draw(), CFeatGlyph::x_isDrawn(), ILayoutPolicy::x_SeparateObjects(), and CLayoutGroup::x_UpdateBoundingBox().

◆ GetModelRect()

TModelRect CSeqGlyph::GetModelRect ( ) const

inline

◆ GetNeighbours()

CSeqGlyph::ENeighbours CSeqGlyph::GetNeighbours ( ) const

inline

Definition at line 630 of file seq_glyph.hpp.

References m_Neighbours.

◆ GetParent() [1/2]

CSeqGlyph * CSeqGlyph::GetParent ( void )

inline

Definition at line 626 of file seq_glyph.hpp.

References m_Parent.

◆ GetParent() [2/2]

const CSeqGlyph * CSeqGlyph::GetParent ( void ) const

inline

Definition at line 622 of file seq_glyph.hpp.

References m_Parent.

Referenced by CLayoutGroup::PropagateRelatedSelection(), CSeqGraphicPane::TTHH_GetTooltip(), CGlyphSearchVisitor::Visit(), CSeqGraphicPane::x_GetCachedTipId(), CBinsGlyph::x_GetColorTheme(), CGeneMarkerGlyph::x_GetColorTheme(), CScatterPlotGlyph::x_GetColorTheme(), CFeatGlyph::x_isCollapsible(), CFeatGlyph::x_isExpandable(), CFeatGlyph::x_RedundantLabelCheck(), and CVcfGlyph::x_RedundantLabelCheck().

◆ GetPName()

virtual string CSeqGlyph::GetPName ( ) const

inlinevirtual

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)

Reimplemented in CFeatGlyph.

Definition at line 296 of file seq_glyph.hpp.

◆ GetPos()

const TModelPoint & CSeqGlyph::GetPos ( void ) const

inline

Definition at line 611 of file seq_glyph.hpp.

References m_Pos.

◆ GetPosInWorld()

void CSeqGlyph::GetPosInWorld ( TModelPoint & pos ) const

inline

Get top left position in world coordinate.

Definition at line 615 of file seq_glyph.hpp.

References CGlPoint< T >::Init(), m_Pos, CGlPoint< T >::X(), and x_Local2World().

Referenced by CLayoutTrackHandler::x_MoveTrackDownRecursive(), CLayoutTrackHandler::x_MoveTrackUpRecursive(), CFeaturePanel::x_RenderFeatureGrid(), and CLayoutTrackHandler::x_StartMoving().

◆ GetRange()

TSeqRange CSeqGlyph::GetRange ( void ) const

inlinevirtual

get the total range of this object.

CSeqGlyph inline methods.

Reimplemented in CDummyGlyph, CVisRangeGlyph, CVcfGlyph, CSegmentGlyph, CRsitesGlyph, CMatePairGlyph, CHistogramGlyph, CLinkedFeatsGroup, CGeneGroup, CFeatGlyph, CClonePlacementGlyph, CAlignGlyph, CLDBlockGlyph, CScatterPlotGlyph, CGeneMarkerGlyph, and CBinsGlyph.

Definition at line 513 of file seq_glyph.hpp.

References m_Pos, m_Width, and CGlPoint< T >::X().

Referenced by LessBySeqPos(), LessBySeqSize(), CSeqGraphicPane::OnLeftDblClick(), CSeqGraphicPane::OnLeftUp(), SGlyphRangeSorter::operator()(), CSeqGraphicPane::SelectOnlyThisObject(), CInlineLayout::x_BuildLayoutMultiRows(), CSeqGraphicPane::x_ChangeSwitchPoint(), CGeneModelFeatJob::x_CreateGeneModels(), CAlignSmearGlyph::x_Draw(), CLayoutGroup::x_Draw(), x_DrawInnerLabelColumns(), x_DrawInnerLabels(), x_InitHTMLActiveArea(), and CCommentGlyph::x_UpdateBoundingBox().

◆ GetRenderingContext()

const CRenderingContext * CSeqGlyph::GetRenderingContext ( ) const

inline

Get the rendering context.

Definition at line 690 of file seq_glyph.hpp.

References m_Context.

Referenced by CBinsGlyph::GetHTMLActiveAreas(), CGeneMarkerGlyph::GetHTMLActiveAreas(), CFeatGlyph::GetTooltip(), CHistogramGlyph::x_DrawDataPoints(), CVcfGlyph::x_DrawHighlight(), CSnpTrack::x_IsOverviewMode(), CLayoutTrackHandler::x_StartMoving(), CLDBlockTrack::x_UpdateData(), and CSnpTrack::x_UpdateData().

◆ GetRight()

TModelUnit CSeqGlyph::GetRight ( ) const

inlinevirtual

Definition at line 603 of file seq_glyph.hpp.

References m_Pos, m_Width, and CGlPoint< T >::X().

Referenced by CColumnLayout::BuildLayout(), CCompactLayout::BuildLayout(), CLegendItemGlyph::GetHTMLActiveAreas(), CMatePairGlyph::GetTooltip(), IsIn(), IsInHor(), LessByPos(), SGlyphSorter::operator()(), CInlineLayout::x_BuildLayout1Row(), CInlineLayout::x_BuildLayoutMultiRows(), CScatterPlotGlyph::x_Draw(), CClonePlacementGlyph::x_Draw(), CCommentGlyph::x_Draw(), CGeneGroup::x_Draw(), CNamedGroup::x_Draw(), CSegmentGlyph::x_Draw(), CFeatGlyph::x_DrawAdditionalInfo(), CVcfGlyph::x_DrawAdditionalInfo(), CAlignGlyph::x_DrawAlignRowSequence(), CAlnStatGlyph::x_DrawBarGraph(), CLayoutGroup::x_DrawBoundary(), CAlnStatGlyph::x_DrawDensityTable(), x_DrawException(), CLinkedFeatsGroup::x_DrawLabels(), CFeatGlyph::x_DrawLabelWithYPinned(), CVcfGlyph::x_DrawLabelWithYPinned(), CHistogramGlyph::x_DrawLinearRuler(), CHistogramGlyph::x_DrawLogRuler(), CAlignGlyph::x_DrawPWAlign(), CTranslationGlyph::x_DrawSequence(), CLayoutTrack::x_GetTBRect(), x_InitHTMLActiveArea(), CLinkedFeatsGroup::x_LabelFirst(), CLayeredLayout::x_LayerByPos(), CLayeredLayout::x_LayerBySize(), CLayoutTrack::x_RenderTitleBar(), CLinkedFeatsGroup::x_UpdateBoundingBox(), and CGlyphContainer::x_UpdateComments().

◆ GetRowNum()

size_t CSeqGlyph::GetRowNum ( ) const

inline

Definition at line 281 of file seq_glyph.hpp.

References m_RowNumber.

Referenced by GetFadeFactor(), CAlignGlyph::IsLastRow(), and CMatePairGlyph::x_Draw().

◆ GetTearline()

size_t CSeqGlyph::GetTearline ( ) const

inline

Definition at line 736 of file seq_glyph.hpp.

References m_Tearline.

Referenced by CColumnLayout::BuildLayout(), CSimpleLayout::BuildLayout(), GetFadeFactor(), CAlignGlyph::IsLastRow(), CMatePairGlyph::x_Draw(), and CAlignGlyph::x_DrawAlignRowSequence().

◆ GetTearlineText()

string CSeqGlyph::GetTearlineText ( ) const

inline

Definition at line 278 of file seq_glyph.hpp.

References m_sTearlineText.

Referenced by CFeatGlyph::GetLabel().

◆ GetTooltip()

void CSeqGlyph::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 in CVisRangeGlyph, CVcfGlyph, CTranslationGlyph, CSequenceTrack, CSegmentSmearGlyph, CSegmentGlyph, CMatePairGlyph, CLayoutTrack, CLinkedFeatsGroup, CFeatGlyph, CCommentGlyph, CClonePlacementGlyph, CAlignSmearGlyph, CAlignGlyph, CAlnStatGlyph, CLDBlockGlyph, CGeneMarkerGlyph, CBinsGlyph, CTraceGlyph, CHistogramGlyph, and CScatterPlotGlyph.

Definition at line 136 of file seq_glyph.cpp.

Referenced by CCommentGlyph::GetTooltip(), CSeqGraphicRenderer::GetTooltip(), CSeqGraphicPane::TTHH_GetTooltip(), and CAlnVecRow::x_GetAlignmentTooltip().

◆ GetTop()

TModelUnit CSeqGlyph::GetTop ( ) const

inlinevirtual

Definition at line 599 of file seq_glyph.hpp.

References m_Pos, and CGlPoint< T >::Y().

Referenced by IsIn(), CLayoutTrack::MoveTo(), CBinsGlyph::x_Draw(), CGeneMarkerGlyph::x_Draw(), CScatterPlotGlyph::x_Draw(), CLDBlockGlyph::x_Draw(), CAlignGlyph::x_Draw(), CCdsGlyph::x_Draw(), CClonePlacementGlyph::x_Draw(), CCommentGlyph::x_Draw(), CFeatGlyph::x_Draw(), CGeneGroup::x_Draw(), CLinkedFeatsGroup::x_Draw(), CHistogramGlyph::x_Draw(), CLayoutGroup::x_Draw(), CLayoutTrack::x_Draw(), CLegendItemGlyph::x_Draw(), CNamedGroup::x_Draw(), CRsitesGlyph::x_Draw(), CSegmentGlyph::x_Draw(), CSegmentSmearGlyph::x_Draw(), CTranslationGlyph::x_Draw(), CVcfGlyph::x_Draw(), CAlnStatGlyph::x_DrawBarGraph(), CAlnStatGlyph::x_DrawDensityTable(), x_DrawException(), CSegmentSmearGlyph::x_DrawGaps(), CHistogramGlyph::x_DrawGraphMap(), CFeaturePanel::x_DrawHairLine(), CHistogramGlyph::x_DrawHeatMap(), CHistogramGlyph::x_DrawLinearRuler(), CHistogramGlyph::x_DrawLogRuler(), CFeatGlyph::x_DrawProjectedRuler(), CFeatGlyph::x_DrawRuler(), CHistogramGlyph::x_DrawSmoothCurve(), x_Local2World(), CLayoutTrackHandler::x_Move(), CVarTrack::x_OnJobCompleted(), CFeaturePanel::x_RenderFeatureGrid(), CGraphOverlay::x_UpdateBoundingBox(), CGraphTrack::x_UpdateBoundingBox(), CIntronTrack::x_UpdateBoundingBox(), CAlignmentTrack::x_UpdateBoundingBox(), CGeneModelTrack::x_UpdateBoundingBox(), and CGlyphContainer::x_UpdateCommentTargetPos().

◆ GetVisible()

size_t CSeqGlyph::GetVisible ( void ) const

inline

Definition at line 284 of file seq_glyph.hpp.

References m_Visible.

Referenced by CAlignGlyph::GetHTMLActiveAreas(), CAlignGlyph::GetTooltip(), CAlignGlyph::x_Draw(), and CMatePairGlyph::x_Draw().

◆ GetWidth()

TModelUnit CSeqGlyph::GetWidth ( void ) const

inlinevirtual

Definition at line 591 of file seq_glyph.hpp.

References m_Width.

◆ HasSideLabel()

virtual bool CSeqGlyph::HasSideLabel ( ) const

inlinevirtual

Query if there is label and label is on the side.

This method may not be applicable to all different types of glyphs. It is up to the concrete glyph to implement. By default, it returns false. Putting this in this base class is just for the sake of inline layout policy to determine if special actions need to take if there is sided label.

Reimplemented in CVcfGlyph, CSegmentGlyph, CFeatGlyph, and CClonePlacementGlyph.

Definition at line 187 of file seq_glyph.hpp.

◆ HitTest()

CRef< CSeqGlyph > CSeqGlyph::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 in CSequenceTrack, CLayoutGroup, CGraphOverlay, CGlyphContainer, CLinkedFeatsGroup, and CFeaturePanel.

Definition at line 106 of file seq_glyph.cpp.

References IsIn(), and CRef< C, Locker >::Reset().

Referenced by CLayoutGroup::HitTest().

◆ HitTestHor()

bool CSeqGlyph::HitTestHor	(	TSeqPos	x,
		const CObject *	obj
	)

virtual

Reimplemented in CVcfGlyph, CLayoutGroup, CGlyphContainer, CFeaturePanel, and CFeatGlyph.

Definition at line 115 of file seq_glyph.cpp.

References IsInHor().

Referenced by CVcfGlyph::HitTestHor().

◆ Intersects()

bool CSeqGlyph::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 in CLayoutGroup, CGlyphContainer, and CLinkedFeatsGroup.

Definition at line 120 of file seq_glyph.cpp.

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

◆ IsClickable()

virtual bool CSeqGlyph::IsClickable ( ) const

inlinevirtual

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 in CVisRangeGlyph, CVcfGlyph, CTranslationGlyph, CTraceGlyph, CSegmentSmearGlyph, CSegmentGlyph, CMatePairGlyph, CLegendItemGlyph, CHistogramGlyph, CLinkedFeatsGroup, CFeatGlyph, CClonePlacementGlyph, CAlignSmearGlyph, CAlignGlyph, CAlnStatGlyph, CLDBlockGlyph, CScatterPlotGlyph, CGeneMarkerGlyph, and CBinsGlyph.

Definition at line 195 of file seq_glyph.hpp.

Referenced by CSeqGraphicPane::OnMotion(), and CAlnVecRow::OnMouseEvent().

◆ IsHighlighted()

bool CSeqGlyph::IsHighlighted ( ) const

inline

Definition at line 577 of file seq_glyph.hpp.

References m_Highlighted.

Referenced by Draw(), CLinkedFeatsGroup::GetHTMLActiveAreas(), SGlyphByPos::operator()(), SGlyphBySize::operator()(), SGlyphBySeqPos::operator()(), SGlyphBySeqSize::operator()(), SGlyphBySeqPos::s_CompareCRefs(), SGlyphBySeqSize::s_CompareCRefs(), CLinkedFeatsGroup::Update(), CGeneModelTrack::x_AddLandMarkFeaturesLayout(), CGeneGroup::x_Draw(), CLinkedFeatsGroup::x_Draw(), CLinkedFeatsGroup::x_DrawLabels(), CLinkedFeatsGroup::x_GetUniqueLabel(), and CLinkedFeatsGroup::x_UpdateBoundingBox().

◆ IsIn() [1/2]

bool CSeqGlyph::IsIn ( const TModelPoint & p ) const

inline

Hit test for points in PARENT COORD.

Definition at line 569 of file seq_glyph.hpp.

References CGlPoint< T >::X(), and CGlPoint< T >::Y().

Referenced by CLinkedFeatsGroup::HitTest(), CGlyphContainer::HitTest(), CGraphOverlay::HitTest(), CLayoutGroup::HitTest(), HitTest(), and CSequenceTrack::HitTest().

◆ IsIn() [2/2]

bool CSeqGlyph::IsIn	(	TModelUnit	x,
		TModelUnit	y
	)		const

Definition at line 142 of file seq_glyph.cpp.

References GetBottom(), GetLeft(), GetRight(), GetTop(), m_Context, and CRenderingContext::ScreenToSeq().

◆ IsInHor()

bool CSeqGlyph::IsInHor ( TModelUnit x ) const

Definition at line 149 of file seq_glyph.cpp.

References GetLeft(), GetRight(), m_Context, and CRenderingContext::ScreenToSeq().

Referenced by CFeatGlyph::HitTestHor(), CGlyphContainer::HitTestHor(), CLayoutGroup::HitTestHor(), and HitTestHor().

◆ IsSelected()

bool CSeqGlyph::IsSelected ( ) const

inline

Definition at line 573 of file seq_glyph.hpp.

References m_Selected.

Referenced by CLinkedFeatsGroup::GetHTMLActiveAreas(), CLinkedFeatsGroup::GetTooltip(), CLinkedFeatsGroup::HitTest(), CFeatGlyph::SetSelected(), CLinkedFeatsGroup::SetSelected(), CVcfGlyph::SetSelected(), CLinkedFeatsGroup::Update(), CSelectionVisitor::Visit(), CSelectionVisitor::x_DoSelection(), CAlignSmearGlyph::x_Draw(), CClonePlacementGlyph::x_Draw(), CCommentGlyph::x_Draw(), CFeatGlyph::x_Draw(), CLinkedFeatsGroup::x_Draw(), CHistogramGlyph::x_Draw(), CMatePairGlyph::x_Draw(), CSegmentGlyph::x_Draw(), CVcfGlyph::x_Draw(), CFeatGlyph::x_DrawAdditionalInfo(), CVcfGlyph::x_DrawAdditionalInfo(), CLayoutGroup::x_DrawBoundary(), CLinkedFeatsGroup::x_DrawLabels(), CFeatGlyph::x_DrawLabelWithXPinned(), CVcfGlyph::x_DrawLabelWithXPinned(), CFeatGlyph::x_DrawLabelWithYPinned(), CVcfGlyph::x_DrawLabelWithYPinned(), CAlignGlyph::x_DrawMultiAlign(), CAlignGlyph::x_DrawMultiAlignLabel(), CAlignGlyph::x_DrawPWAlign(), CLinkedFeatsGroup::x_GetUniqueLabel(), CClonePlacementGlyph::x_ShowLabel(), CFeatGlyph::x_ShowLabel(), CVcfGlyph::x_ShowLabel(), CFeatGlyph::x_ShowRuler(), and CLinkedFeatsGroup::x_UpdateBoundingBox().

◆ LessByPos()

bool CSeqGlyph::LessByPos ( const CSeqGlyph & obj ) const

inline

compare this object to another, based on glyph geometry position.

Notice that glyph geometry position may be the same as sequence position if there is not additional visual features showing up at the start and the end of the glyph. E.g. the possible visual featue can be the side label.

Definition at line 543 of file seq_glyph.hpp.

References GetLeft(), and GetRight().

Referenced by SGlyphByPos::operator()(), and operator<().

◆ LessBySeqPos()

bool CSeqGlyph::LessBySeqPos ( const CSeqGlyph & obj ) const

inlinevirtual

compare this object to another based on glyph sequence position.

Reimplemented in CVcfGlyph, CFeatGlyph, and CAlignGlyph.

Definition at line 534 of file seq_glyph.hpp.

References GetRange(), r0, and r1.

Referenced by CAlignGlyph::LessBySeqPos(), CFeatGlyph::LessBySeqPos(), CVcfGlyph::LessBySeqPos(), SGlyphBySeqPos::operator()(), SLandmarkFeatBySeqPos::operator()(), and SGlyphBySeqPos::s_CompareCRefs().

◆ LessBySeqSize()

bool CSeqGlyph::LessBySeqSize ( const CSeqGlyph & obj ) const

inline

compare this object to another, based on sequence size.

Definition at line 550 of file seq_glyph.hpp.

References GetLength(), COpenRange< Position >::GetLength(), and GetRange().

Referenced by SGlyphBySeqSize::operator()(), and SGlyphBySeqSize::s_CompareCRefs().

◆ LessBySize()

bool CSeqGlyph::LessBySize ( const CSeqGlyph & obj ) const

inline

compare this object to another, based on geometry size.

Notice that sequence size and glyph geometry size may be the same for some cases.

Definition at line 556 of file seq_glyph.hpp.

References GetWidth(), and m_Width.

Referenced by SGlyphBySize::operator()().

◆ NeedTooltip()

bool CSeqGlyph::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 in CVisRangeGlyph, CTranslationGlyph, CTraceGlyph, CSequenceTrack, CSegmentSmearGlyph, CSegmentGlyph, CRsitesGlyph, CMatePairGlyph, CLayoutTrack, CHistogramGlyph, CLinkedFeatsGroup, CCommentGlyph, CClonePlacementGlyph, CAlignSmearGlyph, CAlignGlyph, CAlnStatGlyph, CLDBlockGlyph, CScatterPlotGlyph, CGeneMarkerGlyph, CBinsGlyph, CVcfGlyph, and CFeatGlyph.

Definition at line 130 of file seq_glyph.cpp.

◆ OnContextMenu()

bool CSeqGlyph::OnContextMenu ( wxContextMenuEvent & event )

virtual

Reimplemented in CLegendItemGlyph.

Definition at line 81 of file seq_glyph.cpp.

Referenced by CSeqGraphicPane::OnContextMenu().

◆ OnLeftDblClick()

bool CSeqGlyph::OnLeftDblClick ( const TModelPoint & )

virtual

Reimplemented in CSequenceTrack, CLayoutTrack, CAlnStatGlyph, CLDBlockGlyph, CGeneMarkerGlyph, CBinsGlyph, CTraceGlyph, CLegendItemGlyph, CHistogramGlyph, and CScatterPlotGlyph.

Definition at line 76 of file seq_glyph.cpp.

Referenced by CSeqGraphicPane::OnLeftDblClick(), and CAlnVecRow::OnMouseEvent().

◆ OnLeftDown()

bool CSeqGlyph::OnLeftDown ( const TModelPoint & )

virtual

Reimplemented in CLayoutTrack.

Definition at line 64 of file seq_glyph.cpp.

Referenced by CSeqGraphicPane::OnLeftDown(), and CAlnVecRow::OnMouseEvent().

◆ OnLeftUp()

bool CSeqGlyph::OnLeftUp ( const TModelPoint & )

virtual

Definition at line 70 of file seq_glyph.cpp.

Referenced by CAlnVecRow::OnMouseEvent().

◆ PointInRect() [1/2]

bool CSeqGlyph::PointInRect	(	const TModelPoint &	p,
		const TModelRect &	rc
	)

inlinestatic

Definition at line 694 of file seq_glyph.hpp.

References CGlPoint< T >::X(), and CGlPoint< T >::Y().

Referenced by CLayoutTrack::OnLeftDown(), CLayoutTrack::x_HitIconTest(), and CLayoutTrack::x_HitTitleBar().

◆ PointInRect() [2/2]

bool CSeqGlyph::PointInRect	(	TModelUnit	x,
		TModelUnit	y,
		const TModelRect &	rc
	)

inlinestatic

Definition at line 698 of file seq_glyph.hpp.

References b, CGlRect< T >::Bottom(), l(), CGlRect< T >::Left(), r(), CGlRect< T >::Right(), swap(), t, and CGlRect< T >::Top().

◆ SetHeight()

void CSeqGlyph::SetHeight ( TModelUnit h )

inlinevirtual

Definition at line 650 of file seq_glyph.hpp.

References m_Height.

◆ SetHideLabel()

virtual void CSeqGlyph::SetHideLabel ( bool )

inlinevirtual

Force to hide label.

This method may not be applicable to all different types of glyphs. It is up to the concrete glyph to implement. By default, it does nothing. Putting this in the base class is just for the sake of inline layout policy to make sure not overlaping between glyph's label and other glyphs or lables.

Reimplemented in CVcfGlyph, CSegmentGlyph, CFeatGlyph, and CClonePlacementGlyph.

Definition at line 179 of file seq_glyph.hpp.

Referenced by CInlineLayout::x_BuildLayout1Row(), CInlineLayout::x_BuildLayoutMultiRows(), CFeatureTrack::x_InitGlyphs_Recursive(), and CVcfTrack::x_OnJobCompleted().

◆ SetHighlighted()

void CSeqGlyph::SetHighlighted ( bool flag )

inline

Definition at line 634 of file seq_glyph.hpp.

References m_Highlighted.

Referenced by CGeneModelTrack::x_AddLandMarkFeaturesLayout(), CSegmentMapTrack::x_AddSegmentMapLayout(), and CFeatureTrack::x_InitGlyphs_Recursive().

◆ SetHighlightsColor() [1/2]

void CSeqGlyph::SetHighlightsColor ( const CRgbaColor & hl_color )

inline

Definition at line 640 of file seq_glyph.hpp.

References m_HighlightsColor.

Referenced by CGeneModelTrack::x_AddLandMarkFeaturesLayout(), CSegmentMapTrack::x_AddSegmentMapLayout(), CTrackContainer::x_AddSubtrack(), and CFeatureTrack::x_InitGlyphs_Recursive().

◆ SetHighlightsColor() [2/2]

void CSeqGlyph::SetHighlightsColor ( const string & hl_color_str )

Definition at line 156 of file seq_glyph.cpp.

References Error(), LOG_POST, and m_HighlightsColor.

◆ SetLeft()

void CSeqGlyph::SetLeft ( TModelUnit l )

inlinevirtual

Definition at line 654 of file seq_glyph.hpp.

References l(), m_Pos, and CGlPoint< T >::m_X.

◆ SetLevel()

void CSeqGlyph::SetLevel ( int Level )

inline

Definition at line 287 of file seq_glyph.hpp.

References m_Level.

Referenced by CFeatureTrack::x_AddHistogram(), CSGFeatureJob::x_CreateFeature_Recursive(), ILayoutPolicy::x_SeparateObjects(), and CLayoutGroup::x_UpdateBoundingBox().

◆ SetNeighbours()

void CSeqGlyph::SetNeighbours ( CSeqGlyph::ENeighbours neighbours )

inline

Definition at line 674 of file seq_glyph.hpp.

References m_Neighbours.

Referenced by CInlineLayout::x_BuildLayoutMultiRows().

◆ SetParent() [1/2]

void CSeqGlyph::SetParent ( CSeqGlyph * p )

inline

◆ SetParent() [2/2]

CSeqGlyph * CSeqGlyph::SetParent ( void )

inline

Definition at line 666 of file seq_glyph.hpp.

References m_Parent.

◆ SetPos()

void CSeqGlyph::SetPos ( const TModelPoint & upper_left )

inlinevirtual

Definition at line 662 of file seq_glyph.hpp.

References m_Pos.

Referenced by CLayoutTrackHandler::x_StartMoving().

◆ SetRender()

void CSeqGlyph::SetRender ( IGlyphRenderer * renderer )

inline

set customized renderer for this layout objects.

Definition at line 680 of file seq_glyph.hpp.

References m_Renderer.

◆ SetRenderingContext()

void CSeqGlyph::SetRenderingContext ( CRenderingContext * context )

inline

◆ SetRowNum()

void CSeqGlyph::SetRowNum ( size_t cur_row )

inline

Definition at line 280 of file seq_glyph.hpp.

References m_RowNumber.

Referenced by CLayeredLayout::x_LayerBySize().

◆ SetSelected()

bool CSeqGlyph::SetSelected ( bool flag )

inlinevirtual

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 in CVcfGlyph, CLinkedFeatsGroup, and CFeatGlyph.

Definition at line 525 of file seq_glyph.hpp.

References m_Selected.

Referenced by CFeatGlyph::SetSelected(), CLinkedFeatsGroup::SetSelected(), CVcfGlyph::SetSelected(), CSelectionVisitor::Visit(), and CSelectionVisitor::x_DoSelection().

◆ SetTearline()

void CSeqGlyph::SetTearline ( size_t Tearline )

inline

tearline factor – used to limit a list of glyphs

Definition at line 730 of file seq_glyph.hpp.

References m_Tearline.

Referenced by CColumnLayout::BuildLayout(), CSGAlignmentJob::x_GetAlignments(), and CAlignmentTrack::x_OnLayoutPolicyChanged().

◆ SetTearlineText()

void CSeqGlyph::SetTearlineText ( const string & sTearlineText )

inline

tearline text – if set, is appended to the glyph name (does not naffect processing otherwise)

Definition at line 277 of file seq_glyph.hpp.

References m_sTearlineText.

Referenced by CSGFeatureJob::x_CreateFeature_Recursive().

◆ SetTop()

void CSeqGlyph::SetTop ( TModelUnit b )

inlinevirtual

Definition at line 658 of file seq_glyph.hpp.

References m_Pos, CGlPoint< T >::m_Y, and t.

Referenced by CCompactLayout::BuildLayout(), CFeaturePanel::CFeaturePanel(), CLayoutTrack::MoveTo(), CInlineLayout::x_BuildLayout1Row(), CInlineLayout::x_BuildLayoutMultiRows(), CLayoutTrackHandler::x_Move(), CFeatGlyph::x_UpdateBoundingBox(), CLinkedFeatsGroup::x_UpdateBoundingBox(), CGlyphContainer::x_UpdateBoundingBox(), CGraphOverlay::x_UpdateBoundingBox(), CGraphTrack::x_UpdateBoundingBox(), CIntronTrack::x_UpdateBoundingBox(), CLayoutGroup::x_UpdateBoundingBox(), CSequenceTrack::x_UpdateBoundingBox(), CVcfGlyph::x_UpdateBoundingBox(), CDummyTrack::x_UpdateBoundingBox(), CAlignmentTrack::x_UpdateBoundingBox(), CGeneModelTrack::x_UpdateBoundingBox(), CGlyphContainer::x_UpdateComments(), CGraphOverlay::x_UpdateLegend(), and CHistogramGlyph::x_UpdateLegend().

◆ SetVisible()

void CSeqGlyph::SetVisible ( size_t v )

inline

Definition at line 283 of file seq_glyph.hpp.

References m_Visible.

Referenced by CColumnLayout::BuildLayout().

◆ SetWidth()

void CSeqGlyph::SetWidth ( TModelUnit w )

inlinevirtual

Definition at line 646 of file seq_glyph.hpp.

References m_Width.

◆ Update()

void CSeqGlyph::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 in CDummyTrack, CSixFramesTransTrack, CLayoutGroup, CGlyphContainer, CLinkedFeatsGroup, CGeneGroup, CFeaturePanel, and CDataTrack.

Definition at line 86 of file seq_glyph.cpp.

References x_UpdateBoundingBox().

Referenced by CTrackContainer::AddTracks(), CGraphTrack::SetLayout(), CFeaturePanel::Update(), CGeneGroup::Update(), CInlineLayout::x_BuildLayout1Row(), CInlineLayout::x_BuildLayoutMultiRows(), CLayoutTrack::x_Expand(), CLayoutTrackHandler::x_StartMoving(), and CGraphOverlay::x_UpdateTrackSettings().

◆ x_Draw()

virtual void CSeqGlyph::x_Draw ( ) const

protectedpure virtual

The default renderer for this layout object.

Implemented in CDummyGlyph, CVisRangeGlyph, CVcfGlyph, CTranslationGlyph, CTraceGlyph, CSwitchPointGlyph, CSegmentSmearGlyph, CSegmentGlyph, CRsitesGlyph, CNamedGroup, CMatePairGlyph, CLegendItemGlyph, CLayoutTrack, CLayoutGroup, CHistogramGlyph, CLinkedFeatsGroup, CGeneGroup, CFeaturePanel, CFeatGlyph, CCommentGlyph, CClonePlacementGlyph, CCdsGlyph, CAlignSmearGlyph, CAlignGlyph, CAlnStatGlyph, CLDBlockGlyph, CScatterPlotGlyph, CGeneMarkerGlyph, and CBinsGlyph.

Referenced by Draw().

◆ x_DrawException()

void CSeqGlyph::x_DrawException ( ) const

protected

Draw a shading background to indicate exception.

Definition at line 338 of file seq_glyph.cpp.

References IRender::Color4f(), CRenderingContext::DrawQuad(), GetBottom(), CRange_Base::GetFrom(), GetGl(), GetLeft(), GetRight(), CRange_Base::GetTo(), GetTop(), CRenderingContext::IntersectVisible(), m_Context, and CRenderingContext::ScreenToSeq().

Referenced by CFeatGlyph::x_Draw(), and CLinkedFeatsGroup::x_Draw().

◆ x_DrawHighlight()

void CSeqGlyph::x_DrawHighlight ( ) const

protectedvirtual

Reimplemented in CVcfGlyph, CLayoutGroup, and CLinkedFeatsGroup.

Definition at line 170 of file seq_glyph.cpp.

References CRenderingContext::DrawHighlight(), GetModelRect(), m_Context, and m_HighlightsColor.

Referenced by Draw(), and CGeneGroup::x_Draw().

◆ x_DrawInnerLabelColumns()

void CSeqGlyph::x_DrawInnerLabelColumns	(	TModelUnit	base,
		const string &	label,
		const CRgbaColor &	color,
		const CGlTextureFont &	font,
		bool	side_label_visible
	)		const

protected

◆ x_DrawInnerLabels()

void CSeqGlyph::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

protected

◆ x_DrawTruncatedLabel()

void CSeqGlyph::x_DrawTruncatedLabel	(	const string &	label,
		const CGlTextureFont &	font,
		TModelUnit	width,
		TModelUnit	x,
		TModelUnit	y,
		vector< TModelRange > *	labels_ranges = `nullptr`
	)		const

protected

Definition at line 311 of file seq_glyph.cpp.

References GetGl(), label, m_Context, CRenderingContext::ScreenToSeq(), CRenderingContext::SeqToScreen(), CRenderingContext::TextOut(), IRender::TextWidth(), and CGlTextureFont::Truncate().

Referenced by x_DrawInnerLabels().

◆ x_InitHTMLActiveArea()

void CSeqGlyph::x_InitHTMLActiveArea ( CHTMLActiveArea & area ) const

protected

initialize the basic information for a given active area.

Definition at line 380 of file seq_glyph.cpp.

References GetHeight(), GetLeft(), GetRange(), GetRight(), CGlRect< T >::Init(), CRenderingContext::IsFlippedStrand(), CHTMLActiveArea::m_Bounds, m_Context, CHTMLActiveArea::m_SeqRange, CRenderingContext::SeqToScreenXClipped(), and x_Local2World().

◆ x_IntersectVisible()

template<class T >

template bool CSeqGlyph::x_IntersectVisible< TSeqPos >	(	const CRange< T > &	SeqRange,
		T &	from,
		T &	to
	)		const

protected

Definition at line 412 of file seq_glyph.cpp.

References COpenRange< Position >::Empty(), CRange_Base::GetFrom(), CRange_Base::GetTo(), CRenderingContext::IntersectVisible(), and m_Context.

◆ x_Local2World() [1/2]

void CSeqGlyph::x_Local2World ( TModelPoint & p ) const

inlineprotected

Transform the coordiantes from local coord. to world coord.

Definition at line 726 of file seq_glyph.hpp.

References CGlPoint< T >::m_X, and CGlPoint< T >::m_Y.

Referenced by CAlnStatGlyph::GetHTMLActiveAreas(), CHistogramGlyph::GetHTMLActiveAreas(), CMatePairGlyph::GetHTMLActiveAreas(), CNamedGroup::GetHTMLActiveAreas(), CLegendItemGlyph::GetHTMLActiveAreas(), GetPosInWorld(), CFeatGlyph::x_DrawProjectedRuler(), CFeatGlyph::x_DrawRuler(), CHistogramGlyph::x_DrawSmoothCurve(), x_InitHTMLActiveArea(), x_Local2World(), CHistogramGlyph::x_PointToWorld(), and x_Visible_V().

◆ x_Local2World() [2/2]

void CSeqGlyph::x_Local2World	(	TModelUnit &	x,
		TModelUnit &	y
	)		const

protected

Definition at line 371 of file seq_glyph.cpp.

References GetTop(), m_Parent, and x_Local2World().

◆ x_OnLayoutChanged()

void CSeqGlyph::x_OnLayoutChanged ( )

protectedvirtual

update the layout.

Reimplemented in CLayoutTrack, CGraphTrack, and CGraphOverlay.

Definition at line 353 of file seq_glyph.cpp.

References m_Parent, x_OnLayoutChanged(), and x_UpdateBoundingBox().

Referenced by CFeatGlyph::LayoutChanged(), CVcfGlyph::LayoutChanged(), CAlnStatGlyph::OnLeftDblClick(), CHistogramGlyph::RunSettingsDialog(), CFeatGlyph::SetSelected(), CLinkedFeatsGroup::SetSelected(), CLayoutGroup::UpdateLayout(), CLayoutTrack::x_OnLayoutChanged(), and x_OnLayoutChanged().

◆ x_Parent2Local() [1/3]

void CSeqGlyph::x_Parent2Local ( TModelPoint & pnt ) const

inlineprotected

Transform the coordiante from parent coord. to local coord.

Definition at line 710 of file seq_glyph.hpp.

References CGlPoint< T >::m_X, and CGlPoint< T >::m_Y.

Referenced by CLinkedFeatsGroup::HitTest(), CGlyphContainer::HitTest(), CGraphOverlay::HitTest(), CLayoutGroup::HitTest(), CGlyphContainer::Intersects(), CLayoutGroup::Intersects(), and x_World2Local().

◆ x_Parent2Local() [2/3]

void CSeqGlyph::x_Parent2Local ( TModelRect & rect ) const

inlineprotected

Transform the coordiante from parent coord. to local coord.

Definition at line 718 of file seq_glyph.hpp.

References m_Pos, CGlRect< T >::Offset(), and CGlPoint< T >::Y().

◆ x_Parent2Local() [3/3]

void CSeqGlyph::x_Parent2Local	(	TModelUnit &	,
		TModelUnit &	y
	)		const

inlineprotected

Transform the coordiante from parent coord. to local coord.

Definition at line 714 of file seq_glyph.hpp.

References m_Pos, and CGlPoint< T >::Y().

◆ x_UpdateBoundingBox()

virtual void CSeqGlyph::x_UpdateBoundingBox ( )

protectedpure virtual

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

Implemented in CGeneModelTrack, CAlignmentTrack, CDummyTrack, CDummyGlyph, CVisRangeGlyph, CVcfGlyph, CTranslationGlyph, CTraceGraphTrack, CTraceGlyph, CSwitchPointGlyph, CSequenceTrack, CSegmentSmearGlyph, CSegmentGlyph, CRsitesGlyph, CNamedGroup, CMatePairGlyph, CLegendItemGlyph, CLayoutTrack, CLayoutGroup, CIntronTrack, CHistogramGlyph, CGraphTrack, CGraphOverlay, CGlyphContainer, CLinkedFeatsGroup, CFeatGlyph, CCommentGlyph, CClonePlacementGlyph, CCdsGlyph, CAlignSmearGlyph, CAlignGlyph, CAlnStatGlyph, CLDBlockGlyph, CScatterPlotGlyph, CGeneMarkerGlyph, and CBinsGlyph.

Referenced by Update(), and x_OnLayoutChanged().

◆ x_Visible_V()

bool CSeqGlyph::x_Visible_V ( ) const

protected

is this glyph visible in vertical direction?

Definition at line 403 of file seq_glyph.cpp.

References b, COpenRange< Position >::Empty(), GetHeight(), CRenderingContext::IntersectVisible_Y(), m_Context, t, and x_Local2World().

Referenced by CNamedGroup::GetHTMLActiveAreas(), CLayoutGroup::x_Draw(), CLayoutTrack::x_Draw(), and CNamedGroup::x_Draw().

◆ x_World2Local() [1/2]

void CSeqGlyph::x_World2Local ( TModelPoint & p ) const

inlineprotected

Transform the coordiante from world coord. to local coord.

Definition at line 722 of file seq_glyph.hpp.

References CGlPoint< T >::m_X, and CGlPoint< T >::m_Y.

Referenced by CMatePairGlyph::GetTooltip(), CSequenceTrack::GetTooltip(), CSequenceTrack::NeedTooltip(), CLayoutTrack::OnLeftDblClick(), CSequenceTrack::OnLeftDblClick(), CLayoutTrack::OnLeftDown(), CLayoutTrack::OnMotion(), and x_World2Local().

◆ x_World2Local() [2/2]

void CSeqGlyph::x_World2Local	(	TModelUnit &	x,
		TModelUnit &	y
	)		const

protected

Definition at line 362 of file seq_glyph.cpp.

References m_Parent, x_Parent2Local(), and x_World2Local().

Member Data Documentation

◆ m_Context

CRenderingContext* CSeqGlyph::m_Context

protected

the rendering context

Definition at line 346 of file seq_glyph.hpp.

◆ m_Height

TModelUnit CSeqGlyph::m_Height

private

object height

Definition at line 353 of file seq_glyph.hpp.

Referenced by GetBottom(), GetHeight(), GetModelRect(), and SetHeight().

◆ m_Highlighted

bool CSeqGlyph::m_Highlighted

private

Definition at line 358 of file seq_glyph.hpp.

Referenced by IsHighlighted(), and SetHighlighted().

◆ m_HighlightsColor

unique_ptr<CRgbaColor> CSeqGlyph::m_HighlightsColor

protected

Highlight color.

Definition at line 347 of file seq_glyph.hpp.

Referenced by GetHighlightsColor(), SetHighlightsColor(), CGeneModelTrack::x_AddLandMarkFeaturesLayout(), CSegmentMapTrack::x_AddSegmentMapLayout(), x_DrawHighlight(), CGeneModelTrack::x_InitFeature_Recursive(), and CFeatureTrack::x_InitGlyphs_Recursive().

◆ m_Level

int CSeqGlyph::m_Level

private

shows how deep is the glyph in an hierarchy (0 being closer to root, -1 undefined)

Definition at line 371 of file seq_glyph.hpp.

Referenced by GetLevel(), and SetLevel().

◆ m_Neighbours

ENeighbours CSeqGlyph::m_Neighbours

protected

Indicates whether the glyph has neighbours.

Definition at line 348 of file seq_glyph.hpp.

Referenced by GetNeighbours(), SetNeighbours(), and CFeatGlyph::x_DrawFeatureBar().

◆ m_Parent

CSeqGlyph* CSeqGlyph::m_Parent

protected

parent/child relationships for this feature

Definition at line 345 of file seq_glyph.hpp.

Referenced by GetParent(), SetParent(), x_Local2World(), x_OnLayoutChanged(), CFeatGlyph::x_RedundantLabelCheck(), CVcfGlyph::x_RedundantLabelCheck(), and x_World2Local().

◆ m_Pos

TModelPoint CSeqGlyph::m_Pos

private

upper left corner position in parent coord

Definition at line 355 of file seq_glyph.hpp.

Referenced by GetBottom(), GetLeft(), GetModelRect(), GetPos(), GetPosInWorld(), GetRange(), GetRight(), GetTop(), SetLeft(), SetPos(), SetTop(), and x_Parent2Local().

◆ m_Renderer

CIRef<IGlyphRenderer> CSeqGlyph::m_Renderer

private

user-defined renderer

Definition at line 356 of file seq_glyph.hpp.

Referenced by Draw(), and SetRender().

◆ m_RowNumber

size_t CSeqGlyph::m_RowNumber

private

Definition at line 365 of file seq_glyph.hpp.

Referenced by GetRowNum(), and SetRowNum().

◆ m_Selected

bool CSeqGlyph::m_Selected

private

Definition at line 357 of file seq_glyph.hpp.

Referenced by IsSelected(), and SetSelected().

◆ m_sTearlineText

string CSeqGlyph::m_sTearlineText

private

Definition at line 377 of file seq_glyph.hpp.

Referenced by GetTearlineText(), and SetTearlineText().

◆ m_Tearline

size_t CSeqGlyph::m_Tearline

private

Definition at line 361 of file seq_glyph.hpp.

Referenced by GetTearline(), and SetTearline().

◆ m_Visible

bool CSeqGlyph::m_Visible

private

Definition at line 368 of file seq_glyph.hpp.

Referenced by GetVisible(), and SetVisible().

◆ m_Width

TModelUnit CSeqGlyph::m_Width

private

object width

Definition at line 354 of file seq_glyph.hpp.

Referenced by GetModelRect(), GetRange(), GetRight(), GetWidth(), LessBySize(), and SetWidth().

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

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

Classes

Public Types

Public Member Functions

Static Public Member Functions

Protected Member Functions

Protected Attributes

Private Attributes

Additional Inherited Members

Detailed Description

Member Typedef Documentation

◆ TAreaVector

◆ TConstObjects

◆ TObjects

Member Enumeration Documentation

◆ ENeighbours

Constructor & Destructor Documentation

◆ CSeqGlyph()

◆ ~CSeqGlyph()

Member Function Documentation

◆ Accept()

◆ Draw()

◆ GetBottom()

◆ GetFadeFactor()

◆ GetHeight()

◆ GetHighlightsColor()

◆ GetHTMLActiveAreas()

◆ GetLeft()

◆ GetLevel()

◆ GetModelRect()

◆ GetNeighbours()

◆ GetParent() [1/2]

◆ GetParent() [2/2]

◆ GetPName()

◆ GetPos()

◆ GetPosInWorld()

◆ GetRange()

◆ GetRenderingContext()

◆ GetRight()

◆ GetRowNum()

◆ GetTearline()

◆ GetTearlineText()

◆ GetTooltip()

◆ GetTop()

◆ GetVisible()

◆ GetWidth()

◆ HasSideLabel()

◆ HitTest()

◆ HitTestHor()

◆ Intersects()

◆ IsClickable()

◆ IsHighlighted()

◆ IsIn() [1/2]

◆ IsIn() [2/2]

◆ IsInHor()

◆ IsSelected()

◆ LessByPos()

◆ LessBySeqPos()

◆ LessBySeqSize()

◆ LessBySize()

◆ NeedTooltip()

◆ OnContextMenu()

◆ OnLeftDblClick()

◆ OnLeftDown()

◆ OnLeftUp()

◆ PointInRect() [1/2]

◆ PointInRect() [2/2]

◆ SetHeight()

◆ SetHideLabel()

◆ SetHighlighted()

◆ SetHighlightsColor() [1/2]

◆ SetHighlightsColor() [2/2]

◆ SetLeft()

◆ SetLevel()

◆ SetNeighbours()

◆ SetParent() [1/2]

◆ SetParent() [2/2]

◆ SetPos()

◆ SetRender()

◆ SetRenderingContext()

◆ SetRowNum()