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NCBI C++ ToolKit: src/gui/widgets/seq_graphic/vcf_glyph.cpp Source File

& ref_allele,

& alt_alleles) :

m_Object(new

(seq_id, sID, pos, ref_allele, alt_alleles))

m_Intervals.push_back(GetRange());

m_Intervals.push_back(GetRange());

&info_fields =

->GetInfoColumns();

it = info_fields.find(

);

(it != info_fields.end()) {

it = info_fields.find(

);

(it != info_fields.end()) {

clinsig = it->second;

tooltip.

(

,

(clinsig,

,

, str_buff));

it = info_fields.find(

);

(it != info_fields.end()) {

(!str_buff.empty()) {

str_buff[0] =

(str_buff[0]);

tooltip.

(

, str_buff);

it = info_fields.find(

);

(it != info_fields.end()) {

{

,

},

{

,

},

{

,

},

{

,

},

{

,

},

{

,

},

{

,

},

{

,

},

{

,

},

{

,

},

{

,

},

{

,

},

{

,

},

{

,

}

clnvcso_it = sm_CLNVCSO2Type.

(it->second);

(clnvcso_it != sm_CLNVCSO2Type.

())

str_buff = clnvcso_it->second;

(str_buff.empty()) {

it = info_fields.find(

);

(it != info_fields.end() && it->second.empty() ==

) {

str_buff[0] =

(str_buff[0]);

(str_buff.empty())

str_buff =

->GetVariationTypeAsString();

(!str_buff.empty()) {

tooltip.

(

, str_buff);

(!

->GetAltAlleles_display().empty() &&

->GetAltAlleles_display().front() !=

)

allele =

->GetAltAlleles_display().front();

allele =

->GetRefAllele_display();

tooltip.

(

, allele);

it = info_fields.find(

);

(it != info_fields.end()) {

(

& s : v) {

str_buff =

;

tooltip.

(

, str_buff);

&info_fields =

->GetInfoColumns();

(

->IsDbVar() ==

) {

tooltip.

(

,

->GetAllAlleles_display());

all_alt_alleles_same_len(

);

allele_len =

->GetLongestAlleleLen(all_alt_alleles_same_len);

(allele_len > 0) {

var_type_shown{

};

(info_fields.size() > 0) {

(info_fields.count(

)) {

{

,

},

{

,

},

{

,

},

{

,

},

{

,

},

{

,

}

svtype = info_fields.at(

);

(labels.count(svtype) > 0) {

tooltip.

(

, labels.at(svtype));

var_type_shown =

;

(info_fields.count(

))

tooltip.

(

, info_fields.at(

));

(info_fields.count(

))

tooltip.

(

, info_fields.at(

));

(info_fields.count(

))

tooltip.

(

, info_fields.at(

));

(info_fields.count(

)) {

svlen = info_fields.at(

);

(svlen.size() > 0) {

(svlen[0] ==

)

tooltip.

(

, svlen);

(!var_type_shown) {

tooltip.

(

,

->GetVariationTypeAsString());

&info_fields =

->GetInfoColumns();

(info_fields.count(

)) {

dbvarid = info_fields.at(

);

dbvar_link{

};

tooltip.

(

, dbvarid, dbvar_link);

&info_fields =

->GetInfoColumns();

clnsig_it = info_fields.find(

);

clinsig =

;

(clnsig_it != info_fields.end()) {

&info_fields =

->GetInfoColumns();

svtype_it = info_fields.find(

);

sColorKey(

);

(

->GetVariationType()) {

sColorKey =

;

sColorKey =

;

sColorKey =

;

sColorKey =

;

(sColorKey !=

) {

tooltip->SetTrustedData(

);

s = tooltip->Render();

p_areas->push_back(area);

(!

->GetAltAlleles_display().empty() &&

->GetAltAlleles_display().front() !=

)

sAdditionalInfo =

->GetAltAlleles_display().front();

sAdditionalInfo =

->GetRefAllele_display();

sAdditionalInfo.clear();

base += bar_height * 0.5;

(visible_range_pos.

() < min_text_w_pos) {

sAdditionalInfo;

(!sAdditionalInfo.empty()) {

all_same_type =

;

(parent !=

) {

all_same_type =

->AllChildrenSameType();

track_title =

->GetFullTitle();

start_idx =

.find_first_not_of(

);

stop_idx =

.find_last_not_of(

);

= stop_idx-start_idx;

sLabelTextOut;

->

(&font, sLabelTextOut.c_str(), LabelX, LabelY,

,

);

(exon_int.

())

side_lbl{

};

LabelVisibleWidth = (FeatureBarLeft < visible_range.

() ? 0 : FeatureBarLeft - visible_range.

());

LabelVisibleWidth = (FeatureBarRight > visible_range.

() ? 0 : visible_range.

() - FeatureBarRight);

(FeatureBarLeft < visible_range_pos.

() ? 0 : FeatureBarLeft - visible_range_pos.

())

(FeatureBarRight > visible_range_pos.

() ? 0 : visible_range_pos.

() - FeatureBarRight));

(AvailableLabelVisibleWidthPos < m_Context->GetMinLabelWidthPos(font)) {

(label_width_px > max_width_px) {

label_width_px = max_width_px;

fl_content = font.

(fl_content.c_str(), label_width_px);

((string::npos != fl_content.find(

)) && (fl_content.length() <= 5))

label_base += (font_height * 0.5);

label_clear_base = label_base;

(bar_height > font_height) {

label_clear_height = bar_height;

label_clear_base = floor(base) + (label_clear_height * 0.5);

label_x_pos = visible_range_pos.

();

(label_x_pos >

()) {

(label_x_pos, label_clear_base + 1, label_x_pos + label_width_pos,

label_clear_base - label_clear_height - 1), 0);

label_x_pos = visible_range_pos.

() - label_width_pos;

label_clear_base - label_clear_height - 1), 0);

label_base,

,

);

sAdditionalInfo;

(sAdditionalInfo.empty())

(FeatureBarLeft < visible_range.

() ? 0 : FeatureBarLeft - visible_range.

())

(FeatureBarRight > visible_range.

() ? 0 : visible_range.

() - FeatureBarRight));

(AvailableAdditionalInfoVisibleWidthPos < m_Context->GetMinLabelWidthPos(font)) {

(info_width_px > max_width_px) {

info_width_px = max_width_px;

sAdditionalInfo = font.

(sAdditionalInfo.c_str(), info_width_px);

info_base += (font_height * 0.5);

info_clear_base = info_base;

(bar_height > font_height) {

info_clear_height = bar_height;

info_clear_base = floor(base) + (info_clear_height * 0.5);

info_x_pos = visible_range.

();

(info_x_pos, info_clear_base + 1, info_x_pos + info_width_pos,

info_clear_base - info_clear_height - 1), 0);

info_x_pos = visible_range.

() - info_width_pos;

info_clear_base - info_clear_height - 1), 0);

->

(&font, sAdditionalInfo.c_str(), info_x_pos, info_base,

,

);

->

(SeqPosTriangleMidPointX, BoundaryYLow, SeqPosTriangleMidPointX, BoundaryYHigh);

SeqPosTriangleMidPointX + SeqTriangleHalf, BoundaryYLow - TriangleOffsetY,

SeqPosTriangleMidPointX - SeqTriangleHalf, BoundaryYLow - TriangleOffsetY);

SeqPosTriangleMidPointX + SeqTriangleHalf, BoundaryYHigh + TriangleOffsetY,

SeqPosTriangleMidPointX - SeqTriangleHalf, BoundaryYHigh + TriangleOffsetY);

SeqPosTriangleMidPointX + SeqTriangleHalf, BoundaryYLow - TriangleOffsetY,

SeqPosTriangleMidPointX - SeqTriangleHalf, BoundaryYLow - TriangleOffsetY);

BoundaryYLow = YCenterLine - bar_height * 0.5f;

BoundaryYHigh = YCenterLine + bar_height * 0.5f;

x_IntersectVisible<TSeqPos>(SeqRange, SeqPosFrom, SeqPosTo);

gl.

(color_insert);

((SeqPosFrom + SeqPosTo) * 0.5 + 0.5, BoundaryYLow, BoundaryYHigh, YCenterLine);

gl.

(color_delete);

((SeqPosFrom + SeqPosTo) * 0.5 + 0.5, BoundaryYLow, BoundaryYHigh);

->

(SeqPosFrom, BoundaryYLow, SeqPosTo, BoundaryYHigh,

);

shown =

;

(label_width > available_width) {

((string::npos != fl_content.find(

)) && (fl_content.length() <= 5))

User-defined methods of the data storage class.

User-defined methods of the data storage class.

User-defined methods of the data storage class.

User-defined methods of the data storage class.

User-defined methods of the data storage class.

User-defined methods of the data storage class.

static void redundant(Char *flag)

TModelUnit m_OverviewFactor

ratio to bar height

CGlTextureFont m_LabelFont

TModelUnit GetBarHeight(bool overview) const

ELabelPosition m_LabelPos

TModelUnit m_BarHeight

absolute size (in pixel)

@ ePos_Side

always on 5' side

@ ePos_Inside

inside the rendered bar

@ ePos_Above

above the rendered bar

static CGuiRegistry & GetInstance()

access the application-wide singleton

string m_Descr

description that can be used as label or tooltip

bool m_PositiveStrand

the default is true

CLayoutGroup is a container of CSeqGlyphs (layout objects).

static string GetVcfVariantSignature(const objects::CVcfVariant &vcf_variant, objects::CScope *scope)

class CRegistryReadView provides a nested hierarchical view at a particular key.

void TextOut(const CGlTextureFont *font, const char *text, TModelUnit x, TModelUnit y, bool center, bool adjust_flip=true) const

static const int kLabelSpacePx

extra space for side labeling, in screen pixels

void DrawTriangle(TModelUnit x1, TModelUnit y1, TModelUnit x2, TModelUnit y2, TModelUnit x3, TModelUnit y3, bool border=false) const

void DrawHighlight(const TModelRect &rect, const CRgbaColor *color=0) const

const TSeqRange & GetVisSeqRange() const

TModelRange IntersectVisible(const CSeqGlyph *obj) const

TModelUnit GetMinLabelWidthPos() const

void DrawLine(TModelUnit x1, TModelUnit y1, TModelUnit x2, TModelUnit y2) const

objects::CScope & GetScope()

TModelUnit GetVisibleTo() const

void DrawQuad(const TModelRect &rc, bool border=false) const

void DrawSelection(const TModelRect &rc) const

TModelUnit SeqToScreen(const TModelUnit &size) const

convert from sequence positions to screen pixels

TModelUnit GetMaxLabelWidth(const CGlBitmapFont &font) const

In screen pixel..

TModelUnit ScreenToSeq(const TModelUnit &size) const

convert from screen pixels to sequence positions

bool IsOverviewMode() const

const CRgbaColor & GetSelLabelColor() const

bool WillLabelFit(const TModelRect &rc) const

void Draw3DQuad(TModelUnit x1, TModelUnit y1, TModelUnit x2, TModelUnit y2, const CRgbaColor &color, bool border=false) const

void DrawBackground(const TModelRect &rcm, TModelUnit border) const

class CRgbaColor provides a simple abstraction for managing colors.

static CRegistryReadView GetColorReadView(const CGuiRegistry &reg, const string &base_key, const string &sect, const string &key, const string &def_sect="")

Create a read view specifically for 'Color' section.

static void GetColor(const CRegistryReadView &view, const string &key, CRgbaColor &color)

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

void x_InitHTMLActiveArea(CHTMLActiveArea &area) const

initialize the basic information for a given active area.

CRenderingContext * m_Context

the rendering context

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

virtual void x_OnLayoutChanged()

update the layout.

virtual void SetHeight(TModelUnit h)

const CRenderingContext * GetRenderingContext() const

Get the rendering context.

virtual TModelUnit GetRight() 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

virtual void SetWidth(TModelUnit w)

CSeqGlyph * m_Parent

parent/child relationships for this feature

virtual void SetLeft(TModelUnit l)

virtual TModelUnit GetTop() const

virtual TModelUnit GetHeight() const

virtual bool LessBySeqPos(const CSeqGlyph &obj) const

compare this object to another based on glyph sequence position.

virtual void SetTop(TModelUnit b)

virtual bool SetSelected(bool flag)

Select or deselect this glyph.

virtual TModelUnit GetWidth() const

virtual TModelUnit GetLeft() const

TModelRect GetModelRect() const

get the bounding box.

vector< CHTMLActiveArea > TAreaVector

const CSeqGlyph * GetParent(void) const

void GetLabel(string &label, CLabel::ELabelType type) const

retrieve label for a given type

CConstRef< objects::CVcfVariant > m_Object

void x_DrawDeletion(TModelUnit SeqPosTriangleMidPointX, TModelUnit BoundaryYLow, TModelUnit BoundaryYHigh) const

virtual void GetObjects(vector< CConstRef< CObject > > &objs) const

retrieve CObjects corresponding to this CSeqGlyph.

virtual const TIntervals & GetIntervals(void) const

access sub-intervals (if any).

void GetAdditionalInfo(string &sAdditionalInfo) const

variation additional info on the right (alleles)

bool x_LabelOnLeft() const

true if a label should be placed to the left of the feature bar (provided that it is ePos_Side)

void x_DrawLabelWithYPinned(TModelUnit base) const

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

Get the tooltip if available.

virtual void x_Draw() const

The default renderer for this layout object.

void x_DrawInsertion(TModelUnit SeqPosTriangleMidPointX, TModelUnit BoundaryYLow, TModelUnit BoundaryYHigh, TModelUnit YCenterLine) const

void LayoutChanged()

update the layout for everything encompassing this glyph

void x_DrawAdditionalInfo(TModelUnit base) const

TModelUnit x_GetBarHeight() const

virtual void GetHTMLActiveAreas(TAreaVector *p_areas) const

Get html active areas.

void x_DrawLabelWithXPinned(TModelUnit &base) const

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

virtual void SetHideLabel(bool b)

Force to hide label.

bool x_RedundantLabelCheck(const string &label) const

bool x_isDrawn() const

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

virtual void x_DrawHighlight() const

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

access the position of this object.

virtual bool IsClickable() const

Query if this glyph is clickable.

virtual bool LessBySeqPos(const CSeqGlyph &obj) const

compare this object to another based on glyph sequence position.

void x_GetClinVarToolTip(ITooltipFormatter &tooltip) const

void x_MaybeDrawLabelAbove(TModelUnit &base) const

virtual string GetSignature() const

return signature for this glyph.

bool GetCustomColor(CRgbaColor &color) const

Get the customized color for a given feature.

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

Check if need to show tooltip.

void x_DrawInnerLabels(TModelUnit base, vector< TModelRange > *labels_range=nullptr, TSeqRange *interval=nullptr) const

virtual CConstRef< CObject > GetObject(TSeqPos pos) const

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

virtual bool HasSideLabel() const

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

CVcfGlyph(objects::CSeq_id &seq_id, const string &sID, size_t pos, const string &ref_allele, const string &alt_alleles)

alternative alleles separated by /

virtual bool HasObject(CConstRef< CObject > obj) const

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

void x_DrawVariationBar(TModelUnit base) const

virtual void x_UpdateBoundingBox()

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

void x_MaybeDrawLabelOthers(TModelUnit base) const

CConstRef< CFeatureParams > m_Config

virtual bool SetSelected(bool f)

Select or deselect this glyph.

unique_ptr< CRgbaColor > m_CustomColorPtr

virtual TSeqRange GetRange(void) const

get the total range of this object.

vector< TSeqRange > TIntervals

const_iterator end() const

const_iterator find(const key_type &key) const

bool Empty(const CNcbiOstrstream &src)

unsigned int TSeqPos

Type for sequence locations and lengths.

IRender & GetGl()

convenience function for getting current render manager

virtual TModelUnit TextHeight(const CGlTextureFont *font) const =0

virtual TModelUnit TextWidth(const CGlTextureFont *font, const char *text) const =0

CGlRect< TModelUnit > TModelRect

CGlPoint< TModelUnit > TModelPoint

virtual void ColorC(const CRgbaColor &c)=0

Set current color (glColor{3,4}{f,d}{v,})

string Truncate(const char *text, TModelUnit w, ETruncate trunc=eTruncate_Ellipsis) const

Truncate text to the secified width.

CRgbaColor ContrastingColor(bool onlyBW=true) const

Return a color guaranteed to contrast nicely with this color.

static const string snpURL

virtual void AddRow(const string &sContents="", unsigned colspan=2)=0

add a row with a cell, spanning across all columns

static string SelectClinSigTerm(const string &clinsig)

returns the term with the highest pathogenicity if the CLNSIG string has multiple parts (terms)

static CIRef< ITooltipFormatter > CreateTooltipFormatter(ETooltipFormatters)

factory for requested tooltip formatter creation

virtual void AddLinksTitle(const string &sTitle)=0

add a row with the links title

virtual void SetTrustedData(bool trusted_data)

indicates whether the data is coming from a trusted source

virtual void AddLinkRow(const string &sTag, const string &sValue, unsigned valueColWidth=200)=0

add a row with two columns

static const string ClinVarIdURL

standard NCBI resourse URLs

virtual string CreateNcbiLink(const string &sText, const string &sUrl) const =0

construct the HTML code for a link from the displayed text label and supplied NCBI URL path

@ eTooltipFormatter_CSSTable

generated table is CSS based, generated NCBI URLs are paths (recommended for SViewer)

ENa_strand GetStrand(const CSeq_loc &loc, CScope *scope=0)

Returns eNa_strand_unknown if multiple Bioseqs in loc Returns eNa_strand_other if multiple strands in...

position_type GetLength(void) const

TThisType IntersectionWith(const TThisType &r) const

position_type GetToOpen(void) const

#define END_NCBI_SCOPE

End previously defined NCBI scope.

#define BEGIN_NCBI_SCOPE

Define ncbi namespace.

static string SizetToString(size_t value, TNumToStringFlags flags=0, int base=10)

Convert size_t to string.

static list< string > & Split(const CTempString str, const CTempString delim, list< string > &arr, TSplitFlags flags=0, vector< SIZE_TYPE > *token_pos=NULL)

Split a string using specified delimiters.

static SIZE_TYPE FindNoCase(const CTempString str, const CTempString pattern, SIZE_TYPE start, SIZE_TYPE end, EOccurrence which=eFirst)

Find the pattern in the specified range of a string using a case insensitive search.

static string HtmlEncode(const CTempString str, THtmlEncode flags=fHtmlEnc_EncodeAll)

Encode a string for HTML.

static string Join(const TContainer &arr, const CTempString &delim)

Join strings using the specified delimiter.

static string & Replace(const string &src, const string &search, const string &replace, string &dst, SIZE_TYPE start_pos=0, SIZE_TYPE max_replace=0, SIZE_TYPE *num_replace=0)

Replace occurrences of a substring within a string.

static bool SplitInTwo(const CTempString str, const CTempString delim, string &str1, string &str2, TSplitFlags flags=0)

Split a string into two pieces using the specified delimiters.

static enable_if< is_arithmetic< TNumeric >::value||is_convertible< TNumeric, Int8 >::value, string >::type NumericToString(TNumeric value, TNumToStringFlags flags=0, int base=10)

Convert numeric value to string.

static string & ReplaceInPlace(string &src, const string &search, const string &replace, SIZE_TYPE start_pos=0, SIZE_TYPE max_replace=0, SIZE_TYPE *num_replace=0)

Replace occurrences of a substring within a string.

static string & ToUpper(string &str)

Convert string to upper case – string& version.

@ fSplit_Tokenize

All delimiters are merged and trimmed, to get non-empty tokens only.

@ fWithCommas

Use commas as thousands separator.

static const char label[]

TTo GetTo(void) const

Get the To member data.

TFrom GetFrom(void) const

Get the From member data.

ENa_strand

strand of nucleic acid

@ eType_snv

delta=[morph of length 1] NOTE: this is snV not snP; the latter requires frequency-based validation t...

@ eType_mnp

delta=[morph of length >1]

@ eType_delins

delta=[del, ins]

static void text(MDB_val *v)

double r(size_t dimension_, const Int4 *score_, const double *prob_, double theta_)

static SLJIT_INLINE sljit_ins lg(sljit_gpr r, sljit_s32 d, sljit_gpr x, sljit_gpr b)

static const float kMinScaleForRulerLabels

Shoudl match feature_ds.cpp::kMinScaleForMapping i.e.

static const TModelUnit kRSiteMarkerThreshold

Restriction sites marker visibility threshold (ie if the marker's width is smaller then the threshold...

static const int kVertSpace

vertical space between elements.

static const TModelUnit kRSiteMarkerWidth

Restriction sites marker width (absolute)

static const int kRulerHeight

feature ruler height.

static const TModelUnit kRSiteMarkerHeight

Restriction sites marker height (relative to the height of the bar)

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