NCBI C++ ToolKit
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CLinkedFeatsGroup Class Reference

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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< CHTMLActiveAreaTAreaVector
 
typedef list< CRef< CSeqGlyph > > TObjects
 
typedef list< CConstRef< CSeqGlyph > > TConstObjects
 
- Public Types inherited from CObject
enum  EAllocFillMode { eAllocFillNone = 1 , eAllocFillZero , eAllocFillPattern }
 Control filling of newly allocated memory. More...
 
typedef CObjectCounterLocker TLockerType
 Default locker type for CRef. More...
 
typedef atomic< Uint8TCounter
 Counter type is CAtomiCounter. More...
 
typedef Uint8 TCount
 Alias for value type of counter. More...
 
- Public Types inherited from IObjectBasedGlyph
typedef vector< TSeqRangeTIntervals
 

Public Member Functions

 CLinkedFeatsGroup ()
 CLinkedFeatsGroup implementations. More...
 
virtual ~CLinkedFeatsGroup (void)
 
void SetConfig (const CFeatureParams *conf)
 
CLayoutGroupSetGroup ()
 
void SetParentFeat (const CFeatGlyph *feat)
 
CConstRef< CFeatGlyphGetParentFeat () 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< CSeqGlyphHitTest (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< CObjectGetObject (TSeqPos pos) const
 access our core component - we wrap an object(s) of some sort. More...
 
virtual void GetObjects (vector< CConstRef< CObject > > &objs) const
 retrieve CObjects corresponding to this CSeqGlyph. More...
 
virtual bool HasObject (CConstRef< CObject > obj) const
 check if the wrapped object(s) is the one. More...
 
virtual string GetSignature () const
 return signature for this glyph. More...
 
virtual const TIntervalsGetIntervals () const
 access sub-intervals (if any). More...
 
delegate methods of CLayoutGroup
const ILayoutPolicy::TObjectListGetChildren () const
 CLinkedFeatsGroup inline methods. More...
 
ILayoutPolicy::TObjectListSetChildren ()
 
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 CRenderingContextGetRenderingContext () const
 Get the rendering context. More...
 
void SetTearline (size_t Tearline)
 tearline factor – used to limit a list of glyphs More...
 
size_t GetTearline () const
 
void SetTearlineText (const string &sTearlineText)
 tearline text – if set, is appended to the glyph name (does not naffect processing otherwise) More...
 
string GetTearlineText () const
 
void SetRowNum (size_t cur_row)
 
size_t GetRowNum () const
 
void SetVisible (size_t v)
 
size_t GetVisible () const
 
int GetLevel () const
 
void SetLevel (int Level)
 
virtual string GetPName () const
 persistent name of the glyph should not depend on the instance of the glyph, but should uniquely reflect its contents so two glyphs having the same contents will have the same name currently used to track isDrawn() status for expandable glyphs default implementation returns an empty string implementations exist for CFeatGlyph (name of the contained feature) and CLayoutGroup (concatenation of all sorted children names) More...
 
float GetFadeFactor () const
 
virtual bool OnLeftDown (const TModelPoint &)
 
virtual bool OnLeftUp (const TModelPoint &)
 
virtual bool OnLeftDblClick (const TModelPoint &)
 
virtual bool OnContextMenu (wxContextMenuEvent &event)
 
bool IsSelected () const
 
bool IsHighlighted () const
 
CRgbaColorGetHighlightsColor () const
 
virtual TModelUnit GetHeight () const
 
virtual TModelUnit GetWidth () const
 
virtual TModelUnit GetLeft () const
 
virtual TModelUnit GetTop () const
 
virtual TModelUnit GetRight () const
 
virtual TModelUnit GetBottom () const
 
const TModelPointGetPos () const
 
void GetPosInWorld (TModelPoint &pos) const
 Get top left position in world coordinate. More...
 
const CSeqGlyphGetParent (void) const
 
CSeqGlyphGetParent (void)
 
ENeighbours GetNeighbours () const
 
void SetHighlighted (bool flag)
 
void SetHighlightsColor (const CRgbaColor &hl_color)
 
void SetHighlightsColor (const string &hl_color_str)
 
virtual void SetWidth (TModelUnit w)
 
virtual void SetHeight (TModelUnit h)
 
virtual void SetLeft (TModelUnit l)
 
virtual void SetTop (TModelUnit b)
 
virtual void SetPos (const TModelPoint &upper_left)
 
void SetParent (CSeqGlyph *p)
 
CSeqGlyphSetParent (void)
 
void SetNeighbours (ENeighbours neighbours)
 
- Public Member Functions inherited from CObjectEx
 CObjectEx (void)
 
virtual ~CObjectEx (void)
 
- Public Member Functions inherited from CObject
 CObject (void)
 Constructor. More...
 
 CObject (const CObject &src)
 Copy constructor. More...
 
virtual ~CObject (void)
 Destructor. More...
 
CObjectoperator= (const CObject &src) THROWS_NONE
 Assignment operator. More...
 
bool CanBeDeleted (void) const THROWS_NONE
 Check if object can be deleted. More...
 
bool IsAllocatedInPool (void) const THROWS_NONE
 Check if object is allocated in memory pool (not system heap) More...
 
bool Referenced (void) const THROWS_NONE
 Check if object is referenced. More...
 
bool ReferencedOnlyOnce (void) const THROWS_NONE
 Check if object is referenced only once. More...
 
void AddReference (void) const
 Add reference to object. More...
 
void RemoveReference (void) const
 Remove reference to object. More...
 
void ReleaseReference (void) const
 Remove reference without deleting object. More...
 
virtual void DoNotDeleteThisObject (void)
 Mark this object as not allocated in heap – do not delete this object. More...
 
virtual void DoDeleteThisObject (void)
 Mark this object as allocated in heap – object can be deleted. More...
 
void * operator new (size_t size)
 Define new operator for memory allocation. More...
 
void * operator new[] (size_t size)
 Define new[] operator for 'array' memory allocation. More...
 
void operator delete (void *ptr)
 Define delete operator for memory deallocation. More...
 
void operator delete[] (void *ptr)
 Define delete[] operator for memory deallocation. More...
 
void * operator new (size_t size, void *place)
 Define new operator. More...
 
void operator delete (void *ptr, void *place)
 Define delete operator. More...
 
void * operator new (size_t size, CObjectMemoryPool *place)
 Define new operator using memory pool. More...
 
void operator delete (void *ptr, CObjectMemoryPool *place)
 Define delete operator. More...
 
virtual void DebugDump (CDebugDumpContext ddc, unsigned int depth) const
 Define method for dumping debug information. More...
 
- Public Member Functions inherited from CDebugDumpable
 CDebugDumpable (void)
 
virtual ~CDebugDumpable (void)
 
void DebugDumpText (ostream &out, const string &bundle, unsigned int depth) const
 
void DebugDumpFormat (CDebugDumpFormatter &ddf, const string &bundle, unsigned int depth) const
 
void DumpToConsole (void) const
 
- Public Member Functions inherited from CWeakObject
 CWeakObject (void)
 
virtual ~CWeakObject (void)
 
CPtrToObjectProxyGetPtrProxy (void) const
 Get pointer to proxy object containing pointer to this object. More...
 
- Public Member Functions inherited from IObjectBasedGlyph
virtual ~IObjectBasedGlyph ()
 

Protected Member Functions

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< intTCounts
 

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 CFeatGlyphx_GetFirstFeat () const
 get the first feature glyph in the group. More...
 
const CFeatGlyphx_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< CFeatGlyphm_ParentFeat
 
FLabelType m_LabelType
 
CConstRef< CFeatureParamsm_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
CSeqGlyphm_Parent
 parent/child relationships for this feature More...
 
CRenderingContextm_Context
 the rendering context More...
 
unique_ptr< CRgbaColorm_HighlightsColor
 Highlight color. More...
 
ENeighbours m_Neighbours
 Indicates whether the glyph has neighbours. More...
 

Detailed Description

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

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

◆ GetHTMLActiveAreas()

void CLinkedFeatsGroup::GetHTMLActiveAreas ( TAreaVector ) const
virtual

◆ 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

◆ 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

◆ 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

◆ 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_onlyif 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

◆ 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

◆ x_DrawChildrenOnParent()

void CLinkedFeatsGroup::x_DrawChildrenOnParent ( TModelUnit base) const
private

◆ x_DrawFeatureBar()

void CLinkedFeatsGroup::x_DrawFeatureBar ( TModelUnit base) const
private

◆ 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.

References IRender::ColorC(), CRgbaColor::ContrastingColor(), CRenderingContext::DrawBackground(), CSeqFeatData_Base::e_Variation, CLabel::eContent, CLabel::eContentAndProduct, eNa_strand_minus, CFeatureParams::ePos_Above, CFeatureParams::ePos_Inside, CFeatureParams::ePos_Side, CSeqFeatData::eSubtype_cdregion, fLabel_FeatNum, CLayoutGroup::GetChild(), GetChildren(), CLayoutGroup::GetChildrenNum(), CFeatGlyph::GetFeature(), CRange_Base::GetFrom(), GetGl(), CFeatGlyph::GetLabel(), COpenRange< Position >::GetLength(), GetLocation(), CRenderingContext::GetMaxLabelWidth(), CSeqGlyph::GetRight(), CRenderingContext::GetSelLabelColor(), GetStrand(), COpenRange< Position >::GetToOpen(), CRenderingContext::IntersectVisible(), CSeqGlyph::IsHighlighted(), CSeqGlyph::IsSelected(), ITERATE, kEmptyStr, kLabelSpace, label, CGlRect< T >::Left(), CFeatureParams::m_BarHeight, CFeatureParams::m_bgColor, m_Config, CSeqGlyph::m_Context, CFeatureParams::m_fgColor, m_FirstIsParent, m_Group, m_Intervals, CFeatureParams::m_LabelColor, CFeatureParams::m_LabelFont, CFeatureParams::m_LabelPos, m_LabelType, m_ParentFeat, NStr::NumericToString(), CRenderingContext::ScreenToSeq(), CRenderingContext::SeqToScreen(), IRender::TextHeight(), CRenderingContext::TextOut(), IRender::TextWidth(), CGlTextureFont::Truncate(), CRenderingContext::WillLabelFit(), CSeqGlyph::x_DrawInnerLabels(), x_GetFirstFeat(), x_GetLabelHeight(), x_GetUniqueLabel(), x_LabelFirst(), and x_ShowLabel().

Referenced by x_Draw().

◆ x_GetFirstFeat()

const CFeatGlyph * CLinkedFeatsGroup::x_GetFirstFeat ( ) const
private

◆ 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

◆ x_LabelFirst()

bool CLinkedFeatsGroup::x_LabelFirst ( ) const
private

◆ x_ShowLabel()

bool CLinkedFeatsGroup::x_ShowLabel ( ) const
private

◆ x_UpdateBoundingBox()

void CLinkedFeatsGroup::x_UpdateBoundingBox ( )
protectedvirtual

Member Data Documentation

◆ m_Config

CConstRef<CFeatureParams> CLinkedFeatsGroup::m_Config
private

◆ 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

◆ 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

◆ m_LabelType

FLabelType CLinkedFeatsGroup::m_LabelType
private

◆ 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

◆ 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:
Modified on Wed Jul 17 13:18:12 2024 by modify_doxy.py rev. 669887