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CCdsGlyph Class Reference

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

+ Inheritance diagram for CCdsGlyph:
+ Collaboration diagram for CCdsGlyph:

Public Member Functions

void SetCdsConfig (CCdsConfig *config)
 CCdsGlyph inline methods. More...
 
ctors.
 CCdsGlyph (const objects::CMappedFeat &feat)
 
 CCdsGlyph (const objects::CMappedFeat &feat, const objects::CSeq_loc &loc)
 
- Public Member Functions inherited from CFeatGlyph
TIntervalsSetIntervals ()
 CFeatGlyph inline implementations. More...
 
const objects::CSeq_feat & GetFeature (void) const
 Access the original feature. More...
 
const objects::CMappedFeat & GetMappedFeature (void) const
 Access a new, fully remapped feature. More...
 
bool IsLabelHided () const
 
TModelUnit GetBarCenter () const
 
void GetLabel (string &label, CLabel::ELabelType type) const
 retrieve feature label for a given type More...
 
virtual void GetAccessoryLabel (string &accessory_label) const
 Some features may have an accessory label on top (e.g. introns) More...
 
void GetAdditionalInfo (string &sAdditionalInfo) const
 Some features may have additional info on the right (alleles for SNPs) More...
 
virtual bool IsConsensus () const
 Check if (intron) feature is consensus or not. More...
 
bool isRmtBased () const
 
CConstRef< CFeatureParamsGetConfig () const
 
void SetConfig (CConstRef< CFeatureParams > conf)
 
void SetFilter (const string &sFilter)
 sets the filter that was used for creating the track where this feature glyph resides More...
 
void SetRulerType (int ruler_types)
 
void SetProjectedFeat (bool f)
 
bool IsProjectedFeat () const
 
void SetMappingInfo (const TMappingInfo &info)
 
const TMappingInfoGetMappingInfo () const
 
void SetProjectedMappingInfo (const CProjectedMappingInfo &info)
 
const CProjectedMappingInfoGetProjectedMappingInfo () const
 
bool GetCustomColor (CRgbaColor &color) const
 Get the customized color for a given feature. More...
 
void GetCustomColor (size_t idx, CRgbaColor &color) const
 
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...
 
void SetRelatedGlyphSelected (bool Selected)
 
bool GetRelatedGlyphSelected () const
 
void SetTopLabelPrefix (const char *prefix)
 Set prefix to prepend to labels on top. More...
 
bool isDrawn () const
 determines whether the glyph should be drawn or not at all (currently children of unselected parents when m_LinkedFeat is set to "Expandable") More...
 
void LayoutChanged ()
 update the layout for everything encompassing this glyph More...
 
 CFeatGlyph (const objects::CMappedFeat &feat, ELinkedFeatDisplay LinkedFeat=ELinkedFeatDisplay::eLFD_Default)
 
 CFeatGlyph (const objects::CMappedFeat &feat, const objects::CSeq_loc &loc, ELinkedFeatDisplay LinkedFeat=ELinkedFeatDisplay::eLFD_Default)
 
virtual bool NeedTooltip (const TModelPoint &, ITooltipFormatter &, string &) 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 void SetHideLabel (bool b)
 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...
 
virtual bool HitTestHor (TSeqPos x, const CObject *obj)
 
virtual const objects::CSeq_loc & GetLocation (void) const
 access the position of this object. More...
 
virtual CConstRef< CObjectGetObject (TSeqPos pos) const
 Retrieve the feature as an object. 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 (void) const
 access sub-intervals (if any). More...
 
- Public Member Functions inherited from CSeqGlyph
 CSeqGlyph ()
 
virtual ~CSeqGlyph ()
 
virtual CRef< CSeqGlyphHitTest (const TModelPoint &p)
 Hit testing. More...
 
virtual bool Intersects (const TModelRect &rect, TConstObjects &objs) const
 Intersect testing. More...
 
virtual void Update (bool)
 Update content and layout including the bounding box. More...
 
virtual bool Accept (IGlyphVisitor *visitor)
 Interface for accepting an IGlyphVisitor. 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)
 
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

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...
 
- Protected Member Functions inherited from CFeatGlyph
TSeqPos x_GetProtOffset () const
 Returns protein translation offset. More...
 
CRef< objects::CSeq_loc > x_AdjustFrame (const objects::CSeq_loc &loc, TSeqPos offset) const
 Adjusts a location to accommodate for the protein translation offset. More...
 
void x_DrawRuler (TModelUnit base, bool protein_scale=false) const
 
void x_DrawProjectedRuler (TModelUnit base, bool protein_scale=false) const
 
void x_MaybeDrawLabelAbove (TModelUnit &base) const
 
void x_DrawFeatureBar (TModelUnit &base) const
 
void x_DrawFeatureBar_sv (TModelUnit base) const
 
void x_DrawAdditionalInfo (TModelUnit base) const
 
void x_MaybeDrawLabelOthers (TModelUnit base) const
 
void x_DrawRNAProductSequence (TModelUnit base) const
 
bool x_RedundantLabelCheck (const string &label) const
 
void x_DrawInsertion (TModelUnit SeqPosTriangleMidPointX, TModelUnit BoundaryYLow, TModelUnit BoundaryYHigh, TModelUnit YCenterLine) const
 
void x_DrawDeletion (TModelUnit SeqPosTriangleMidPointX, TModelUnit BoundaryYLow, TModelUnit BoundaryYHigh) const
 
void x_DrawRSites (const CRgbaColor &color, TModelUnit BoundaryYLow, TModelUnit BoundaryYHigh) const
 
void x_DrawLabelWithXPinned (TModelUnit &base) const
 
void x_DrawLabelWithYPinned (TModelUnit base) const
 
void x_DrawInnerLabels (TModelUnit base, vector< TModelRange > *labels_range=nullptr, TSeqRange *interval=nullptr) const
 
bool x_isDrawn () const
 determines whether the glyph should be drawn or not at all (currently children of unselected parents when m_LinkedFeat is set to "Expandable") More...
 
bool x_isExpandable (size_t &nChildren) const
 returns true if this glyph is expandable i.e. More...
 
bool x_isCollapsible () const
 returns true if this glyph is collapsible i.e. More...
 
bool x_IsProjected () const
 
bool x_CanShowStrand (objects::ENa_strand strand) const
 
- Protected Member Functions inherited from CSeqGlyph
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

CRef< CCdsConfigm_CdsConfig
 
- Protected Attributes inherited from CFeatGlyph
objects::CMappedFeat m_Feature
 we store a mapped feature object which in turn holds the original feature. More...
 
CConstRef< objects::CSeq_loc > m_Location
 Mapped location in top sequence coordinate. More...
 
TMappingInfo m_MappingInfo
 Feature product sequence mapping info. More...
 
CProjectedMappingInfo m_ProjectedMappingInfo
 
TIntervals m_Intervals
 intervals (like for features or alignments). More...
 
CConstRef< CFeatureParamsm_Config
 All the configs needed for rendering a feature. More...
 
bool m_HideLabel
 Force to hide the label. More...
 
bool m_ProjectedFeat
 Projected features. More...
 
bool m_RSite
 Flag indicating if this is a restriction site. More...
 
int m_RulerType
 
ELinkedFeatDisplay m_LinkedFeat
 linkage mode for the track where this glyph is residing More...
 
string m_sFilter
 filter (if any) for the track where this glyph is residing More...
 
string m_sTopLabelPrefix
 Prefix to prepend to labels on top. More...
 
map< CLabel::ELabelType, stringm_Labels
 
- 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...
 

Private Member Functions

void x_DrawProtSeqWithMapping (TModelUnit trans_y, TModelUnit gen_y, TModelUnit prot_y) const
 
void x_DrawProjectedProtSeq (TModelUnit trans_y, TModelUnit gen_y, TModelUnit prot_y) const
 
void x_PutCodon (const string &codon_str, TSeqPos pos, TModelUnit y, bool neg, bool append) const
 
bool x_WillFit () const
 

Additional Inherited Members

- Public Types inherited from CFeatGlyph
enum  EFeatureParts { eHead_No , eTail_No , eNeedHead , eNeedTail }
 
enum  EUndefinedBpType { eBp_Outer , eBp_Inner , eBp_Unknown }
 
enum  ERulerType { eNoRuler = 0 , eNtRuler = 0x01 , eAaRuler = 0x02 }
 
typedef vector< CRef< CFeatGlyph > > TFeatList
 
typedef CSeqUtils::TMappingInfo TMappingInfo
 
- 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
 
- Static Public Member Functions inherited from CFeatGlyph
static size_t GetCustomColorIdx (const objects::CSeq_feat &feat)
 Get the customized color idx for a given feature. More...
 
static bool IsDbVar (const objects::CSeq_feat &feat)
 Utility to check if a feature is a structural variation. More...
 
- Static Public Member Functions inherited from CSeqGlyph
static bool PointInRect (const TModelPoint &p, const TModelRect &rc)
 
static bool PointInRect (TModelUnit x, TModelUnit y, const TModelRect &rc)
 
- Static Public Member Functions inherited from CObject
static NCBI_XNCBI_EXPORT void ThrowNullPointerException (void)
 Define method to throw null pointer exception. More...
 
static NCBI_XNCBI_EXPORT void ThrowNullPointerException (const type_info &type)
 
static EAllocFillMode GetAllocFillMode (void)
 
static void SetAllocFillMode (EAllocFillMode mode)
 
static void SetAllocFillMode (const string &value)
 Set mode from configuration parameter value. More...
 
- Static Public Member Functions inherited from CDebugDumpable
static void EnableDebugDump (bool on)
 
- Static Public Attributes inherited from CObject
static const TCount eCounterBitsCanBeDeleted = 1 << 0
 Define possible object states. More...
 
static const TCount eCounterBitsInPlainHeap = 1 << 1
 Heap signature was found. More...
 
static const TCount eCounterBitsPlaceMask
 Mask for 'in heap' state flags. More...
 
static const int eCounterStep = 1 << 2
 Skip over the "in heap" bits. More...
 
static const TCount eCounterValid = TCount(1) << (sizeof(TCount) * 8 - 2)
 Minimal value for valid objects (reference counter is zero) Must be a single bit value. More...
 
static const TCount eCounterStateMask
 Valid object, and object in heap. More...
 

Detailed Description

Definition at line 44 of file cds_glyph.hpp.

Constructor & Destructor Documentation

◆ CCdsGlyph() [1/2]

CCdsGlyph::CCdsGlyph ( const objects::CMappedFeat &  feat)

◆ CCdsGlyph() [2/2]

CCdsGlyph::CCdsGlyph ( const objects::CMappedFeat &  feat,
const objects::CSeq_loc &  loc 
)

Member Function Documentation

◆ SetCdsConfig()

void CCdsGlyph::SetCdsConfig ( CCdsConfig config)
inline

CCdsGlyph inline methods.

Definition at line 102 of file cds_glyph.hpp.

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

Referenced by CGeneModelTrack::x_InitFeature_Recursive().

◆ x_Draw()

void CCdsGlyph::x_Draw ( ) const
protectedvirtual

◆ x_DrawProjectedProtSeq()

void CCdsGlyph::x_DrawProjectedProtSeq ( TModelUnit  trans_y,
TModelUnit  gen_y,
TModelUnit  prot_y 
) const
private

◆ x_DrawProtSeqWithMapping()

void CCdsGlyph::x_DrawProtSeqWithMapping ( TModelUnit  trans_y,
TModelUnit  gen_y,
TModelUnit  prot_y 
) const
private

◆ x_PutCodon()

void CCdsGlyph::x_PutCodon ( const string codon_str,
TSeqPos  pos,
TModelUnit  y,
bool  neg,
bool  append 
) const
private

◆ x_UpdateBoundingBox()

void CCdsGlyph::x_UpdateBoundingBox ( )
protectedvirtual

◆ x_WillFit()

bool CCdsGlyph::x_WillFit ( ) const
private

Member Data Documentation

◆ m_CdsConfig

CRef<CCdsConfig> CCdsGlyph::m_CdsConfig
protected

The documentation for this class was generated from the following files:
Modified on Wed May 15 15:03:25 2024 by modify_doxy.py rev. 669887