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

TObjectList::iterator iter =

().begin();

(*iter)->

(layout_only);

min_l =

(min_l, (*iter)->GetLeft());

max_w =

(max_w, (*iter)->GetWidth());

cont = visitor->

(

);

TObjectList::iterator iter =

().begin();

cont = (*iter)->Accept(visitor);

(!linked_feats && !group && !child1->IsSelected()) {

(0)->GetHTMLActiveAreas(p_areas);

(0)->GetHTMLActiveAreas(p_areas);

child1->GetHTMLActiveAreas(p_areas);

TAreaVector::reverse_iterator it_gene = p_areas->rbegin();

it_gene->m_Bounds = p_areas->back().m_Bounds;

<<

(group && group->GetChildren().size() > 2) {

TObjectList::const_iterator iter =

().begin();

gene_highlighted =

;

*

(iter->GetPointer());

(gl.

(&font, gene_label.c_str()) > width) {

gene_label = font.

(gene_label.c_str(), width);

.SetAlpha(0.1f);

.SetAlpha(0.18f);

(gene_highlighted) {

(gl.

(&font, gene_label.c_str()) > width) {

gene_label = font.

(gene_label.c_str(), width);

(gene_label ==

)

feat =

*

(iter->GetPointer());

: m_LabelType(fLabel_ParentLabel)

, m_FirstIsParent(

)

glyph.

(

);

glyph.

(

);

(

== parent_feat) {

first_feat =

;

gui_info(CreateObjectInterface<IGuiObjectInfo>(scoped_obj, &feat_group_params));

gui_info->GetToolTip(tt, t_title, at_p);

gui_info->GetLinks(tt,

);

tt.

(

);

RmtBased{

};

merged_feature_height += 2.0;

.SetBottom(

.Top() + merged_feature_height);

count_set =

;

cont = visitor->

(

);

*

(iter->GetPointer());

(

);

*

(iter->GetPointer());

(

== feat)

base += bar_height * 0.5;

.SetLeft(visible_range.

());

.SetRight(visible_range.

());

curr_idx = num > 1 && neg_strand ? 1 : 0;

curr_idx = 1 - curr_idx;

curr_idx = num > 1 && neg_strand ? 1 : 0;

curr_idx = 1 - curr_idx;

( !label_l.empty() && draw_left ) {

(label_w_l > max_w) {

label_l = font.

(label_l.c_str(), label_w_l);

vis_r.

() + label_w_l, base - height * 0.5);

->

(&font, label_l.c_str(), rect.

(), base + font_h * 0.5,

,

);

( !label_r.empty() && draw_right ) {

(label_w_r > max_w) {

label_r = font.

(label_r.c_str(), label_w_r);

vis_r.

(), base - height * 0.5);

->

(&font, label_r.c_str(), rect.

(), base + font_h * 0.5,

,

);

*

(iter->GetPointer());

line_y1 = line_ym - bar_height * 0.5f;

line_y2 = line_ym + bar_height * 0.5f;

show_strand_indicator =

is_parent =

;

(show_strand_indicator) {

line_y1 = line_ym - bar_height * 0.5f;

line_y2 = line_ym + bar_height * 0.5f;

two_colors =

;

*

(iter->GetPointer());

show_strand_indicator =

max_c = max<float>(max_c, *iter - 1);

(max_c == 0.0f) {

max_c = 1.0f / max_c;

color_lite2 = color2;

first_pass =

;

is_bar_visible = visible_range.

();

(is_bar_visible) {

= visible_range.

() + 1;

(!first_pass && pre_to <

) {

glPushAttrib(GL_LINE_BIT);

gl.

(GL_LINE_STIPPLE);

gl.

(GL_LINE_STIPPLE);

gl.

(GL_LINE_STIPPLE);

gl.

(GL_LINE_STIPPLE);

gl.

(GL_LINE_STIPPLE);

is_intron_visible = visible_range.

();

(is_intron_visible) {

pre_to = visible_range.

();

= visible_range.

();

pre_to + (

- pre_to) * 0.5;

gl.

(GL_LINE_STIPPLE);

gl.

(GL_LINE_STIPPLE);

gl.

(GL_LINE_STIPPLE);

- pre_to, apart, bar_height,

(is_bar_visible) {

first_pass =

;

TIntervalCounts int_counts;

*

(iter->GetPointer());

TIntervalCounts::iterator at_iter = int_counts.find(

);

(at_iter != int_counts.end()) {

at_iter->second += 1;

int_counts[

] = 1;

at_iter = int_counts.find(

);

(at_iter != int_counts.end()) {

at_iter->second -= 1;

int_counts[

] = -1;

(int_counts.size() > 1);

TIntervalCounts::const_iterator s_iter = int_counts.begin();

TIntervalCounts::const_iterator e_iter = s_iter;

= s_iter->second;

(e_iter != int_counts.end()) {

+= s_iter->second;

feat =

*

(iter->GetPointer());

(CLayoutGroup::TObjectList::const_reverse_iterator iter =

().rbegin();

feat =

*

(iter->GetPointer());

(merged_feats_count) {

tooltip->SetTrustedData(

);

s = tooltip->Render();

p_areas->push_back(area);

(children.size() <= 1)

CLayoutGroup::TObjectList::const_iterator feat_it = children.begin();

(++feat_it != children.end()) {

void Add(const CConstRef< objects::CSeq_feat > &feat, const CSeqUtils::TMappingInfo &mapping_info=CSeqUtils::TMappingInfo())

bool IsLabelHided() const

bool GetCustomColor(CRgbaColor &color) const

Get the customized color for a given feature.

virtual string GetSignature() const

return signature for this glyph.

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

Get the tooltip if available.

const TMappingInfo & GetMappingInfo() const

virtual bool HasObject(CConstRef< CObject > obj) const

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

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

retrieve CObjects corresponding to this CSeqGlyph.

virtual CConstRef< CObject > GetObject(TSeqPos pos) const

Retrieve the feature as an object.

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

access the position of this object.

CConstRef< CFeatureParams > GetConfig() const

static bool IsDbVar(const objects::CSeq_feat &feat)

Utility to check if a feature is a structural variation.

const objects::CMappedFeat & GetMappedFeature(void) const

Access a new, fully remapped feature.

virtual TSeqRange GetRange(void) const

get the total range of this object.

virtual const TIntervals & GetIntervals(void) const

access sub-intervals (if any).

const objects::CSeq_feat & GetFeature(void) const

Access the original feature.

static size_t GetCustomColorIdx(const objects::CSeq_feat &feat)

Get the customized color idx for a given feature.

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

retrieve feature label for a given type

EConnection m_Connections

TModelUnit m_LineWidth

absolute value (in pixel)

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

bool m_ShowStrandIndicator

virtual string GetSignature() const

return signature for this glyph.

bool x_ShowGeneLabel() const

virtual const TIntervals & GetIntervals() const

access sub-intervals (if any).

@ eGene_Shown

show gene bar

@ eGene_ShowLabelOnly

hide gene bar, but show label with bar space

@ eGene_Hidden

hide gene bar and gene label completely

virtual CConstRef< CObject > GetObject(TSeqPos pos) const

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

virtual bool Accept(IGlyphVisitor *visitor)

Interface for accepting an IGlyphVisitor.

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

retrieve CObjects corresponding to this CSeqGlyph.

void SetShowGene(bool flag)

virtual const objects::CSeq_loc & GetLocation() const

access the position of this object.

virtual bool HasObject(CConstRef< CObject > obj) const

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

virtual TSeqRange GetRange(void) const

Get gene feature range instead.

virtual void GetHTMLActiveAreas(TAreaVector *p_areas) const

Get html active areas.

virtual void Update(bool layout_only)

CGeneGroup implementations.

virtual void x_Draw() const

The default renderer for this layout object.

TModelUnit x_GetLabelHeight() const

Returns the height of the label with margin included.

const CFeatGlyph * x_GetFirstFeat() const

string m_Descr

description that can be used as label or tooltip

@ fNoCaching

The tooltip for this feature should not be cached.

int m_Flags

area flags, will need to replace m_Type

unsigned m_MergedFeatsCount

bool m_PositiveStrand

the default is true

CLayoutGroup is a container of CSeqGlyphs (layout objects).

void HideMaster(bool hidden=true)

TObjectList & SetChildren()

virtual void x_UpdateBoundingBox()

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

const TObjectList & GetChildren() const

CLayoutGroup inline methods.

void SetAsMaster(CRef< CSeqGlyph > master)

master glyph has some special meaning (e.g.

virtual void GetHTMLActiveAreas(TAreaVector *p_areas) const

Get html active areas.

CConstRef< CSeqGlyph > GetChild(int idx) const

Get the layout object at index 'idx'.

void x_DrawBoundary() const

virtual void Update(bool layout_only)

Update content and layout including the bounding box.

size_t GetChildrenNum() const

Get total number of children.

bool x_isDrawn() const

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

virtual CRef< CSeqGlyph > HitTest(const TModelPoint &p)

Hit testing.

ILayoutPolicy::TObjectList TObjectList

CLinkedFeatsGroup is a container class contains related features.

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

retrieve CObjects corresponding to this CSeqGlyph.

virtual void x_Draw() const

The default renderer for this layout object.

CRef< objects::CSeq_loc > m_Location

just for satisfy IObjectBasedGlyph interface.

TCounts m_IntCounts

Shall have the same size as m_Intervals.

virtual bool Intersects(const TModelRect &rect, TConstObjects &objs) const

Intersect testing.

virtual bool NeedTooltip(const TModelPoint &p, ITooltipFormatter &tt, string &t_title) const

Check if need to show tooltip.

void x_DrawChildrenOnParent(TModelUnit &base) const

draw the merged feature bar with children on top of parent.

CConstRef< CFeatGlyph > m_ParentFeat

virtual void GetHTMLActiveAreas(TAreaVector *p_areas) const

Get html active areas.

virtual bool Accept(IGlyphVisitor *visitor)

Interface for accepting an IGlyphVisitor.

void x_DrawLabels(TModelUnit &base, bool draw_left=true, bool draw_right=true) const

draw the labels for merged features.

void x_CalcIntervals()

calculate the merged feature bar intervals and overlapping counts.

virtual bool IsClickable() const

Query if this glyph is clickable.

CLinkedFeatsGroup()

CLinkedFeatsGroup implementations.

virtual string GetSignature() const

return signature for this glyph.

const ILayoutPolicy::TObjectList & GetChildren() const

CLinkedFeatsGroup inline methods.

bool x_LabelFirst() const

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

bool x_AreAllFeaturesOnSameStrand() const

const CFeatGlyph * x_GetFirstFeat() const

get the first feature glyph in the group.

void x_GetUniqueLabel(string &label) const

utility method for generating a unique label for the merged bar.

bool x_ShowLabel() const

Check if need to show label.

const CFeatGlyph * x_GetLastFeat() const

get the last feature glyph in the group.

virtual bool SetSelected(bool f)

Select or deselect this glyph.

void x_AddFeatHTMLActiveArea(TAreaVector *p_areas, const CFeatGlyph *feat, unsigned merged_feats_count=0) const

virtual void Update(bool layout_only)

Update content and layout including the bounding box.

TModelUnit x_GetLabelHeight() const

Returns the height of the label with margin included.

bool m_FirstIsParent

The first feature is the parent feature.

virtual const objects::CSeq_loc & GetLocation() const

access the position of this object.

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

Get the tooltip if available.

void x_DrawFeatureBar(TModelUnit &base) const

draw the merged feature bar.

virtual bool HasObject(CConstRef< CObject > obj) const

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

virtual void x_UpdateBoundingBox()

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

virtual CRef< CSeqGlyph > HitTest(const TModelPoint &p)

Hit testing.

virtual CConstRef< CObject > GetObject(TSeqPos pos) const

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

virtual TSeqRange GetRange(void) const

get the total range of this object.

virtual const TIntervals & GetIntervals() const

access sub-intervals (if any).

CConstRef< CFeatureParams > m_Config

settings for rendering merged feature bar.

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

void DrawPseudoBar(TModelUnit x1, TModelUnit y1, TModelUnit x2, TModelUnit y2, const CRgbaColor &light_color, const CRgbaColor &dark_color) const

CRef< CSGSequenceDS > GetSeqDS() const

TModelRange IntersectVisible(const CSeqGlyph *obj) const

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

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

void DrawSelection(const TModelRect &rc) const

bool IsSkipFrames() 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

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

void DrawStrandIndicators(const TModelPoint &start, TModelUnit length, TModelUnit apart, TModelUnit size, const CRgbaColor &color, bool neg_strand, bool avoid_center=false, bool single_indicator_center=false, const vector< TModelRange > *labels_ranges=nullptr) const

class CRgbaColor provides a simple abstraction for managing colors.

TSeqPos GetSequenceLength() const

void x_InitHTMLActiveArea(CHTMLActiveArea &area) const

initialize the basic information for a given active area.

CRenderingContext * m_Context

the rendering context

virtual void x_OnLayoutChanged()

update the layout.

void x_Parent2Local(TModelPoint &pnt) const

Transform the coordiante from parent coord. to local coord.

virtual void SetHeight(TModelUnit h)

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

void x_DrawException() const

Draw a shading background to indicate exception.

void SetParent(CSeqGlyph *p)

bool IsIn(const TModelPoint &p) const

Hit test for points in PARENT COORD.

virtual void SetWidth(TModelUnit w)

virtual void SetLeft(TModelUnit l)

virtual TModelUnit GetTop() const

virtual TModelUnit GetHeight() const

virtual void Update(bool)

Update content and layout including the bounding box.

virtual void SetTop(TModelUnit b)

void Draw() const

render the layout.

virtual bool SetSelected(bool flag)

Select or deselect this glyph.

virtual void x_DrawHighlight() const

virtual TModelUnit GetWidth() const

virtual TModelUnit GetLeft() const

TModelRect GetModelRect() const

get the bounding box.

vector< CHTMLActiveArea > TAreaVector

list< CConstRef< CSeqGlyph > > TConstObjects

bool IsHighlighted() const

Visitor interface for applying any potential actions or algorithms.

virtual bool Visit(CSeqGlyph *glyph)=0

list< CRef< CSeqGlyph > > TObjectList

vector< TSeqRange > TIntervals

bool Empty(const CNcbiOstrstream &src)

static DLIST_TYPE *DLIST_NAME() first(DLIST_LIST_TYPE *list)

static const int kLabelSpace

static const int kVertSpace

unsigned int TSeqPos

Type for sequence locations and lengths.

#define ITERATE(Type, Var, Cont)

ITERATE macro to sequence through container elements.

#define LOG_POST(message)

This macro is deprecated and it's strongly recomended to move in all projects (except tests) to macro...

void Error(CExceptionArgs_Base &args)

const string & GetMsg(void) const

Get message string.

static bool IsException(const objects::CSeq_feat &feat)

virtual void Translated(GLdouble x, GLdouble y, GLdouble z)=0

virtual void Translatef(GLfloat x, GLfloat y, GLfloat z)=0

virtual void Enable(GLenum glstate)=0

virtual void LineStipple(GLint factor, GLushort pattern)=0

Set line stipple pattern: glLineStipple(). Deprecated in gl 3.2+.

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

virtual void PopMatrix()=0

void SetFontFace(EFontFace face, bool use_bitmap_overrides=true)

CRange< TModelUnit > TModelRange

void SetFontSize(unsigned int size)

Set/get font size in points.

virtual void Disable(GLenum glstate)=0

glDisable()

virtual void LineWidth(GLfloat w)=0

Set line width for drawing: glLineWidth()

static EFontFace FaceFromString(const string &str)

Selects a font face given a string or eFontFace_LastFont on failure.

CGlPoint< TModelUnit > TModelPoint

virtual void ColorC(const CRgbaColor &c)=0

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

bool Intersects(const CGlRect &R) const

virtual void PushMatrix()=0

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.

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

add a row with a cell, spanning across all columns

static CIRef< ITooltipFormatter > CreateTooltipFormatter(ETooltipFormatters)

factory for requested tooltip formatter creation

void Lighten(float scale)

static CRgbaColor Interpolate(const CRgbaColor &color1, const CRgbaColor &color2, float alpha)

Interpolate two colors.

@ 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...

const CSeq_feat & GetMappedFeature(void) const

Feature mapped to the master sequence.

TObjectType * GetPointer(void) const THROWS_NONE

Get pointer,.

TObjectType * GetPointer(void) THROWS_NONE

Get pointer,.

void Reset(void)

Reset reference object.

position_type GetLength(void) const

bool NotEmpty(void) const

TThisType & CombineWith(const TThisType &r)

position_type GetToOpen(void) const

CRange< TSeqPos > TSeqRange

typedefs for sequence ranges

#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 string LongToString(long value, TNumToStringFlags flags=0, int base=10)

Convert Int to string.

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

Convert int to string.

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 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 const char label[]

TTo GetTo(void) const

Get the To member data.

TFrom GetFrom(void) const

Get the From member data.

@ eNa_strand_both_rev

in reverse orientation

@ eNa_strand_both

in forward orientation

unsigned int

A callback function used to compare two keys in a database.

if(yy_accept[yy_current_state])

static void text(MDB_val *v)

const struct ncbi::grid::netcache::search::fields::SIZE size

const GenericPointer< typename T::ValueType > T2 value

T bound(T x_, T xlo_, T xhi_)

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

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