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NCBI C++ ToolKit: include/gui/widgets/seq_graphic/alignment_glyph.hpp Source File

objects::CSeq_align_Handle& orig_align,

objects::CSeq_align& mapped_align,

objects::CSeq_loc&

(

)

;

objects::CSeq_align& GetAlignment(

)

;

objects::CSeq_align_Handle& GetOrigAlignment(

)

;

TAlnAnchorPair GetAlnAnchorPair(

)

;

GetOrigAnchor(

)

;

ApplyFading()

;

DrawPWAlignElem(

& rcm,

selected,

IsNegative()

;

IsSimplified()

;

()

;

x_DrawPWAlign()

;

x_DrawMultiAlign()

;

override_color,

& read_status_color)

;

override_color,

& read_status_color)

;

x_IsPWAlign()

;

x_CalcIntervals(

& intervals,

target_row = -1)

;

x_ShowLabel()

;

x_ShowScore()

;

x_ShowUnalignedTails(

align_len)

;

x_GetOverrideColor(

& override_color,

reverse_strand =

;

override_color =

;

x_IsSRA()

;

bar_h = floor(bar_h * 0.4);

bar_h = floor(bar_h * 0.2);

@ eExtremeCompact

extreme compact mode

ECompactMode m_CompactMode

Alignment layout compact mode.

class CRgbaColor provides a simple abstraction for managing colors.

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

virtual bool IsClickable() const

Query if this glyph is clickable.

virtual void x_Draw() const =0

The default renderer for this layout object.

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

Get the tooltip if available.

virtual bool NeedTooltip(const TModelPoint &, ITooltipFormatter &, string &) const

Check if need to show tooltip.

virtual TSeqRange GetRange(void) const

get the total range of this object.

virtual bool LessBySeqPos(const CSeqGlyph &obj) const

compare this object to another based on glyph sequence position.

size_t GetTearline() const

virtual void GetHTMLActiveAreas(TAreaVector *) const

Get html active areas.

virtual void x_UpdateBoundingBox()=0

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

IAlnGraphicDataSource - interface to a data source representing an abstract alignment used in graphic...

virtual bool IsNegativeStrand(TNumrow row) const =0

virtual bool IsSimplified() const

bool IsCrossOrigin() const

virtual const TIntervals & GetIntervals(void) const =0

access sub-intervals (if any).

virtual CConstRef< CObject > GetObject(TSeqPos pos) const =0

access our core component - we wrap an object(s) of some sort.

virtual const objects::CSeq_loc & GetLocation(void) const =0

access the position of this object.

virtual string GetSignature() const =0

return signature for this glyph.

virtual bool HasObject(CConstRef< CObject > obj) const =0

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

vector< TSeqRange > TIntervals

virtual IAlnExplorer::TNumrow GetNumRows() const =0

vector< CConstRef< CObject > > GetObjects(CSeq_entry_Handle seh, const string &field, CFieldNamePanel::EFieldType field_type, int subtype, const string &ncRNA_class, CConstRef< objects::CSeq_submit > submit, CRef< CEditingActionConstraint > constraint, vector< CSeq_entry_Handle > *descr_context=nullptr)

unsigned int TSeqPos

Type for sequence locations and lengths.

int TSignedSeqPos

Type for signed sequence position.

bool IsSimplified() const

TAlnAnchorPair GetAlnAnchorPair(void) const

CRange< TModelUnit > TModelRange

TSignedSeqRange aln_range

vector< TModelRange > TMUnitRanges

virtual CConstRef< CObject > GetObject(TSeqPos pos) const

access our core component - we wrap an object(s) of some sort.

TIntervals m_Intervals

intervals.

int GetOrigAnchor(void) const

CRgbaColor read_status_color

const IAlnGraphicDataSource & GetAlignMgr(void) const

Inline methods.

CConstRef< CAlignmentConfig > m_Config

const objects::CSeq_align_Handle & GetOrigAlignment(void) const

CRef< objects::CSeq_loc > m_Location

TModelUnit GetBarHeight() const

void SetConfig(const CAlignmentConfig *conf)

CConstRef< IAlnGraphicDataSource > m_AlnMgr

pointer to the actual alignment information.

pair< CConstRef< CObject >, int > TAlnAnchorPair

bool m_DisableTooltipsCaching

Indicates whether the front-end can cache the tooltips.

vector< CRef< CAlignGlyph > > TAlnList

void SetScore(const ISGAlnScore &score)

const objects::CSeq_align & GetAlignment(void) const

CConstRef< objects::CSeq_align > m_SeqAlign

CConstIRef< ISGAlnScore > m_Score

objects::CSeq_align_Handle m_OrigSeqAlign

int m_OrigAnchor

The anchor row number in original Seq-algin, not alnmgr.

NCBI_XOBJUTIL_EXPORT string GetTitle(const CBioseq_Handle &hnd, TGetTitleFlags flags=0)

void Reset(void)

Reset reference object.

#define END_NCBI_SCOPE

End previously defined NCBI scope.

#define BEGIN_NCBI_SCOPE

Define ncbi namespace.

#define NCBI_GUIWIDGETS_SEQGRAPHIC_EXPORT

Portable reference counted smart and weak pointers using CWeakRef, CRef, CObject and CObjectEx.

#define row(bind, expected)

bool IsLastRow(wxWindow *wnd, wxSizerItemList &itemList)

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