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

vector<SMappedSegment>

objects::CSeq_loc& loc,

objects::CSeq_loc&

(

)

;

objects::CSeq_feat& GetFeature(

)

;

objects::CMappedFeat& GetMappedFeature(

)

;

IsLabelHided()

;

GetAccessoryLabel(

& accessory_label)

;

GetAdditionalInfo(

& sAdditionalInfo)

;

isRmtBased()

;

(

& sFilter) { m_sFilter = sFilter; }

SetRulerType(

ruler_types);

SetProjectedFeat(

);

IsProjectedFeat()

;

SetMappingInfo(

TMappingInfo&

);

TMappingInfo& GetMappingInfo()

;

SetRelatedGlyphSelected(

Selected);

GetRelatedGlyphSelected()

;

SetTopLabelPrefix(

* prefix);

GetCustomColorIdx(

objects::CSeq_feat& feat);

IsDbVar(

objects::CSeq_feat& feat);

LayoutChanged();

()

;

x_GetProtOffset()

;

x_DrawRuler(

base,

protein_scale =

)

;

x_DrawProjectedRuler(

base,

protein_scale =

)

;

x_MaybeDrawLabelAbove(

& base)

;

x_DrawFeatureBar(

& base)

;

x_DrawFeatureBar_sv(

base)

;

x_DrawAdditionalInfo(

base)

;

x_MaybeDrawLabelOthers(

base)

;

x_DrawRNAProductSequence(

base)

;

x_RedundantLabelCheck(

&

)

;

x_DrawInsertion(

SeqPosTriangleMidPointX,

x_DrawDeletion(

SeqPosTriangleMidPointX,

x_DrawLabelWithXPinned(

& base)

;

x_DrawLabelWithYPinned(

base)

;

x_isDrawn()

;

x_isExpandable(

& nChildren)

;

x_isCollapsible()

;

x_IsProjected()

;

EUndefinedBpType x_GetUndefinedBp_from(

objects::CSeq_loc& loc)

;

EUndefinedBpType x_GetUndefinedBp_to(

objects::CSeq_loc& loc)

;

x_ShowLabel()

;

x_LabelOnLeft()

;

x_ShowRuler()

;

x_GetFeatureId()

;

x_GetUserColor(

objects::CUser_object &display_settings,

&

)

;

(*

)(*

, *g1);

}

(idx <

.size()) {

accessory_label.clear();

vector< CRgbaColor > TColorCode

const TColorCode & GetColorCode() const

string m_sTopLabelPrefix

Prefix to prepend to labels on top.

bool IsLabelHided() const

CSeqUtils::TMappingInfo TMappingInfo

TIntervals m_Intervals

intervals (like for features or alignments).

void SetMappingInfo(const TMappingInfo &info)

ELinkedFeatDisplay m_LinkedFeat

linkage mode for the track where this glyph is residing

CConstRef< CFeatureParams > m_Config

All the configs needed for rendering a feature.

CProjectedMappingInfo m_ProjectedMappingInfo

string m_sFilter

filter (if any) for the track where this glyph is residing

void SetRulerType(int ruler_types)

bool GetCustomColor(CRgbaColor &color) const

Get the customized color for a given feature.

TIntervals & SetIntervals()

CFeatGlyph inline implementations.

const CProjectedMappingInfo & GetProjectedMappingInfo() const

objects::CMappedFeat m_Feature

we store a mapped feature object which in turn holds the original feature.

bool IsProjectedFeat() const

const TMappingInfo & GetMappingInfo() const

bool m_ProjectedFeat

Projected features.

bool m_HideLabel

Force to hide the label.

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

access the position of this object.

bool x_HasOuterOnly() const

CFeatGlyph(const objects::CMappedFeat &feat, ELinkedFeatDisplay LinkedFeat=ELinkedFeatDisplay::eLFD_Default)

CConstRef< objects::CSeq_loc > m_Location

Mapped location in top sequence coordinate.

CFeatGlyph(const objects::CMappedFeat &feat, const objects::CSeq_loc &loc, ELinkedFeatDisplay LinkedFeat=ELinkedFeatDisplay::eLFD_Default)

CConstRef< CFeatureParams > GetConfig() const

void SetTopLabelPrefix(const char *prefix)

Set prefix to prepend to labels on top.

void SetProjectedFeat(bool f)

TMappingInfo m_MappingInfo

Feature product sequence mapping info.

vector< CRef< CFeatGlyph > > TFeatList

bool m_RSite

Flag indicating if this is a restriction site.

virtual bool IsConsensus() const

Check if (intron) feature is consensus or not.

void SetFilter(const string &sFilter)

sets the filter that was used for creating the track where this feature glyph resides

void SetConfig(CConstRef< CFeatureParams > conf)

bool isDrawn() const

determines whether the glyph should be drawn or not at all (currently children of unselected parents ...

void SetProjectedMappingInfo(const CProjectedMappingInfo &info)

virtual void GetAccessoryLabel(string &accessory_label) const

Some features may have an accessory label on top (e.g. introns)

bool x_LabelFirst() const

check to see if label needs to be drawn before feature bar.

const objects::CMappedFeat & GetMappedFeature(void) const

Access a new, fully remapped feature.

map< CLabel::ELabelType, string > m_Labels

const objects::CSeq_feat & GetFeature(void) const

Access the original feature.

CRef< CCustomFeatureColor > m_CustomColors

custom color code for features with a special attribute.

void GetAnchorSequence(objects::CScope &scope, string &buffer) const

CConstRef< IAlnGraphicDataSource > m_AlnMgr

void SetAlignmentDataSource(const IAlnGraphicDataSource &align_ds)

CProjectedMappingInfo inline methods.

TSeqRange & GetAnchorRange(const CSeqUtils::TMappingInfo::const_iterator &it) const

const IAlnGraphicDataSource * GetAlignmentDataSource() const

TSeqRange GetMappedProdRange(const CSeqUtils::TMappingInfo::const_iterator &it)

class CRgbaColor provides a simple abstraction for managing colors.

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

virtual string GetPName() const

persistent name of the glyph should not depend on the instance of the glyph, but should uniquely refl...

virtual bool HitTestHor(TSeqPos x, const CObject *obj)

virtual void SetHideLabel(bool)

Force to hide label.

virtual bool IsClickable() const

Query if this glyph is clickable.

virtual void x_Draw() const =0

The default renderer for this layout object.

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

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.

virtual bool HasSideLabel() const

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

virtual bool SetSelected(bool flag)

Select or deselect this glyph.

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.

vector< CHTMLActiveArea > TAreaVector

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

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

static const Colors colors

bool IsConsensus(const CRef< CSeq_id > &seqId)

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)

struct SMappedSegment TMappedSegment

unsigned int TSeqPos

Type for sequence locations and lengths.

vector< TMappedInt > TMappingInfo

string GetLabel(const CSeq_id &id)

TObjectType * GetPointer(void) const THROWS_NONE

Get pointer,.

void Reset(void)

Reset reference object.

static TThisType GetEmpty(void)

#define END_NCBI_SCOPE

End previously defined NCBI scope.

#define BEGIN_NCBI_SCOPE

Define ncbi namespace.

#define NCBI_GUIWIDGETS_SEQGRAPHIC_EXPORT

static const char label[]

ENa_strand

strand of nucleic acid

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

SMappedSegment(CRef< objects::CSeq_interval > product_int, CRef< objects::CSeq_interval > mapped_int, const TSeqRange &anchor_range=TSeqRange::GetEmpty(), const TSeqRange &mapped_range=TSeqRange::GetEmpty())

TSeqRange m_MappedProdRange

CRef< objects::CSeq_interval > m_ProductInt

CRef< objects::CSeq_interval > m_MappedInt

float g0(Seg_Nsm *spn, Thd_Cxe *cxe)

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