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

+ Inheritance diagram for CAlignGlyph:
+ Collaboration diagram for CAlignGlyph:

Classes

struct  SDrawContext
 

Public Types

enum  EAlignSpacing { eOne2One , eOne2Three , eThree2One }
 
typedef vector< CRef< CAlignGlyph > > TAlnList
 
typedef pair< CConstRef< CObject >, intTAlnAnchorPair
 
- 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

 CAlignGlyph (CConstRef< IAlnGraphicDataSource > aln_mgr, const objects::CSeq_align_Handle &orig_align, const objects::CSeq_align &mapped_align, int orig_anchor)
 
const IAlnGraphicDataSourceGetAlignMgr (void) const
 Inline methods. More...
 
const objects::CSeq_align & GetAlignment (void) const
 
const objects::CSeq_align_Handle & GetOrigAlignment (void) const
 
TAlnAnchorPair GetAlnAnchorPair (void) const
 
int GetOrigAnchor (void) const
 
TModelUnit GetBarHeight () const
 
void SetConfig (const CAlignmentConfig *conf)
 
void SetScore (const ISGAlnScore &score)
 
void ApplyFading () const
 
void DrawPWAlignElem (const TModelRect &rcm, bool selected, bool show_label, const CRgbaColor &c_fg, const CRgbaColor &c_seq, const CRgbaColor &c_mis) const
 
void GetTitle (string *title, CLabel::ELabelType type) const
 
bool IsNegative () const
 
void SetShowScore ()
 
bool IsSimplified () const
 
bool IsLastRow () const
 
CSeqGlyph methods
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 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...
 
IObjectBasedGlyph interface implement
virtual const objects::CSeq_loc & GetLocation (void) 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 (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 HitTestHor (TSeqPos x, const CObject *obj)
 
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...
 
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...
 
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

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 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

CConstRef< IAlnGraphicDataSourcem_AlnMgr
 pointer to the actual alignment information. More...
 
CConstRef< objects::CSeq_align > m_SeqAlign
 
objects::CSeq_align_Handle m_OrigSeqAlign
 
int m_OrigAnchor
 The anchor row number in original Seq-algin, not alnmgr. More...
 
CRef< objects::CSeq_loc > m_Location
 
TIntervals m_Intervals
 intervals. More...
 
CConstRef< CAlignmentConfigm_Config
 
CConstIRef< ISGAlnScorem_Score
 
bool m_ShowScore
 
bool m_DisableTooltipsCaching
 Indicates whether the front-end can cache the tooltips. More...
 
float m_FadeFactor
 
- 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 Types

enum  ETail { e5_Prime , e3_Prime }
 
typedef CRange< TModelUnitTModelRange
 
typedef vector< TModelRangeTMUnitRanges
 

Private Member Functions

void x_DrawPWAlign () const
 
void x_DrawMultiAlign () const
 
void x_DrawMultiAlignLabel (int row, TModelUnit y) const
 
void x_DrawAlignRowSequence (TModelUnit center_y, int row, const CRgbaColor &c_fg, const CRgbaColor &c_seq, const CRgbaColor &c_mis) const
 
void x_RenderNonAveragableScores (TModelUnit yy, TSignedSeqRange aln_range, TSeqRange seq_range, TModelUnit height, int row, bool override_color, const CRgbaColor &read_status_color) const
 
void x_RenderAveragableScores (TModelUnit yy, TSignedSeqRange aln_range, TSeqRange seq_range, TModelUnit height, int row, bool override_color, const CRgbaColor &read_status_color) const
 
bool x_IsPWAlign () const
 
void x_CalcIntervals (TIntervals &intervals, int target_row=-1) const
 
bool x_ShowLabel () const
 
bool x_ShowScore () const
 
bool x_ShowUnalignedTails (TModelUnit align_len) const
 
void x_GetOverrideColor (bool &override_color, CRgbaColor &read_status_color) const
 
void x_DrawGaps (const SDrawContext &ctx) const
 
void x_DrawInserts (const SDrawContext &ctx) const
 
void x_DrawIntronsAndInternalUnalignedRegions (const SDrawContext &ctx, TSignedSeqPos from, TSignedSeqPos to) const
 
void x_DrawInternalUnalignedRegions (const SDrawContext &ctx, TMUnitRanges &unaligned_regions) const
 
void x_DrawTailGlyphs (const SDrawContext &ctx, bool show_label, const CRgbaColor &c_fg) const
 
void x_DrawTailSequences (const SDrawContext &ctx, const CRgbaColor &c_fg) const
 
void x_DrawUnalignedBar (const ETail tail, const SDrawContext &ctx, const CRgbaColor &c_fg) const
 
void x_DrawUnalignedRowSequence (const ETail tail, const SDrawContext &ctx, const CRgbaColor &c_fg) const
 
void x_DrawNonConsensusSpliceSites (const SDrawContext &ctx) const
 
void x_DrawNoScoreAlign (const SDrawContext &ctx, const CRgbaColor &c_fg) const
 
void x_DrawStrandIndicators (const SDrawContext &ctx) const
 
void x_DrawSimplified (const SDrawContext &ctx, const CRgbaColor &c_fg) const
 
TSeqRange x_GetAlnTailRange (const ETail tail, const SDrawContext &ctx) const
 
TSeqRange x_ConvertAlnTaillRngToSeqRng (const ETail tail, const SDrawContext &ctx, const TSeqRange &aln_range) const
 
TModelUnit x_GetTailLabelWidth (const TSignedSeqPos tail) const
 
TModelUnit x_GetTailWidth (const TSignedSeqPos tail, const TSignedSeqPos visible_tail, const TSignedSeqPos base_width_curr) const
 
bool x_IsSRA () const
 

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...
 

Detailed Description

Definition at line 70 of file alignment_glyph.hpp.


The documentation for this class was generated from the following files:
Modified on Wed Jul 17 13:17:33 2024 by modify_doxy.py rev. 669887