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

, m_Location(&

.GetLocation())

, m_HideLabel(

)

, m_HideLabel(

)

CreateObjectInterface<IGuiObjectInfo>(scoped_obj,

));

( !gui_info )

;

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

gui_info->GetLinks(tt,

);

p_areas->push_back(area);

(

.IsUser()) {

(

.empty()) {

0xcc, 0xcc, 0xcc, 0xcc, 0xcc, 0xcc, 0xcc, 0xcc,

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0x00, 0x1f, 0xff, 0xc0, 0x00, 0x0f, 0xff, 0xe0,

0x00, 0x07, 0xff, 0xf0, 0x00, 0x03, 0xff, 0xf8,

0x00, 0x01, 0xff, 0xfc, 0x00, 0x00, 0xff, 0xfe,

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0xc0, 0x00, 0x1f, 0xff, 0xe0, 0x00, 0x0f, 0xff,

0xf0, 0x00, 0x07, 0xff, 0xf8, 0x00, 0x03, 0xff,

0xfc, 0x00, 0x01, 0xff, 0xfe, 0x00, 0x00, 0xff,

0xff, 0x00, 0x00, 0x7f, 0xff, 0x80, 0x00, 0x3f,

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0x03, 0xff, 0x03, 0xff, 0x03, 0xff, 0x03, 0xff,

0x03, 0xff, 0x03, 0xff, 0x03, 0xff, 0x03, 0xff,

0x03, 0xff, 0x03, 0xff, 0x03, 0xff, 0x03, 0xff,

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0x03, 0xff, 0x03, 0xff, 0x03, 0xff, 0x03, 0xff,

0x03, 0xff, 0x03, 0xff, 0x03, 0xff, 0x03, 0xff,

0x03, 0xff, 0x03, 0xff, 0x03, 0xff, 0x03, 0xff,

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0x03, 0xff, 0x03, 0xff, 0x03, 0xff, 0x03, 0xff,

0x03, 0xff, 0x03, 0xff, 0x03, 0xff, 0x03, 0xff

line_center = base - head_h * 0.5f;

line_b = line_center + bar_h * 0.5;

line_t = line_center - bar_h * 0.5;

(

.IsClone()) {

}

(

.IsUser()) {

boundary_color.

(0.3f);

== non_prototype_st)

gl.

(highlight_color);

gl.

(GL_POLYGON_STIPPLE);

gl.

(combined_plmt_color);

gl.

(highlight_color);

gl.

(GL_POLYGON_STIPPLE);

(total_range.

() < pix_size) {

total_range.

(), line_b, base_color);

(prototype_ends.size() == 2) {

gl.

(GL_POLYGON_STIPPLE);

gl.

(GL_POLYGON_STIPPLE);

gl.

(boundary_color);

x1 = prototype_ends[0].m_Range.GetToOpen();

x2 = prototype_ends[1].m_Range.GetFrom();

(prototype_ends[0].m_Strand ==

&&

head_len > prototype_ends[0].m_Range.GetLength()) {

x1 = prototype_ends[0].m_Range.GetFrom() + head_len;

(prototype_ends[1].m_Strand ==

&&

head_len > prototype_ends[1].m_Range.GetLength()) {

x2 = prototype_ends[1].m_Range.GetToOpen() - head_len;

gl.

(GL_POLYGON_STIPPLE);

end_uniqueness = unique;

gl.

(boundary_color);

forward = iter->m_Strand ==

;

x2 = x3 - (forward ? head_len : -head_len);

(iter->m_Range.GetLength() < head_len) {

- (forward ? 0.5 : -0.5) * bar_h,

- (forward ? 0.5 : -0.5) * head_h);

gl.

(boundary_color);

0.5 * bar_h, 0.5 * head_h);

gl.

(GL_POLYGON_STIPPLE);

(label_w > widthP) {

(clone_ends.size() == 1) {

(

)clone_ends[1].m_Range.GetFrom());

xM = (in_range.

() + in_range.

() ) * 0.5;

(label_w > max_w) {

(

.GetLength() < label_w) {

gl.

(1.0f, 1.0f, 1.0f);

(label_x, label_b + 1, label_x + label_w,

label_b - 1.0,

,

);

(!

.IsClone())

TStrVector::const_iterator itId;

(itId = nonSupportingIds.begin(); itId != nonSupportingIds.end(); ++itId) {

(supportingIds.count(*itId) == 0)

(uniqueness) {

gl.

(GL_POLYGON_STIPPLE);

gl.

(GL_POLYGON_STIPPLE);

gl.

(GL_POLYGON_STIPPLE);

(prototype_ends[0].m_Strand ==

) {

end_len = prototype_ends[0].m_Range.GetLength();

(extra_space > 0) {

end_num = prototype_ends.size();

(end_num > 1 && prototype_ends[end_num - 1].m_Strand ==

) {

end_len = prototype_ends[end_num - 1].m_Range.GetLength();

(extra_space > 0) {

(prototype_ends.size() == 2) {

(

)prototype_ends[1].m_Range.GetFrom());

(

.IsClone()) {

clone_ends.push_back(end);

prototype_ends.push_back(end);

(clone_ends.empty()) {

(; loc_it && num_loc < 2; ++loc_it, ++num_loc) {

clone_ends.push_back(end);

prototype_ends.push_back(end);

(!clone_ends.empty() &&

.IsUser()) {

(user.

(

) &&

clone_ends[0].m_Uniqueness =

;

(clone_ends.size() > 1 && user.

(

) &&

clone_ends[1].m_Uniqueness =

;

(prototype_ends.empty()) {

(; loc_it && num_loc < 2; ++loc_it, ++num_loc) {

prototype_ends.push_back(end);

User-defined methods of the data storage class.

User-defined methods of the data storage class.

User-defined methods of the data storage class.

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

access the position of this object.

CClonePlacementGlyph(const objects::CMappedFeat &feat)

virtual CConstRef< CObject > GetObject(TSeqPos pos) const

Retrieve the feature as an object.

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

Check if need to show tooltip.

virtual string GetSignature() const

return signature for this glyph.

CConstRef< CClonePlacementParams > m_Config

All the configs needed for rendering a feature.

virtual void SetHideLabel(bool b)

Force to hide label.

const objects::CSeq_feat & GetFeature(void) const

Access the original feature.

virtual void x_UpdateBoundingBox()

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

void x_GetCloneEnds(TCloneEnds &clone_ends, TCloneEnds &prototype_ends) const

virtual bool IsClickable() const

Query if this glyph is clickable.

vector< string > TStrVector

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

retrieve CObjects corresponding to this CSeqGlyph.

virtual TSeqRange GetRange(void) const

get the total range of this object.

objects::CMappedFeat m_Feature

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

virtual void x_Draw() const

The default renderer for this layout object.

virtual const TIntervals & GetIntervals(void) const

access sub-intervals (if any).

virtual void GetHTMLActiveAreas(TAreaVector *p_areas) const

Get html active areas.

CConstRef< objects::CSeq_loc > m_Location

Mapped location in top sequence coordinate.

void x_SetPolygonStipple(EUniqueness uniqueness) const

void x_GetBarSize(TModelUnit &bar_h, TModelUnit &head_h) const

bool x_MatchIds(const TStrSet &supportingIds, const TStrVector &nonSupportingIds) const

const objects::CMappedFeat & GetMappedFeature(void) const

Access a new, fully remapped feature.

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

Get the tooltip if available.

TSeqRange x_GetTotalRange() const

virtual bool HasSideLabel() const

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

virtual bool HasObject(CConstRef< CObject > obj) const

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

bool m_HideLabel

Force to hide the label.

vector< SCloneEnd > TCloneEnds

TIntervals m_Intervals

intervals (like for features or alignments).

ESupportType x_GetSupportTypeForNonPrototypeEnds() const

CGlTextureFont m_LabelFont

CRgbaColor m_UnknownConcordancyColor

TModelUnit m_HeadHeight

absolute size (in pixel)

CRgbaColor m_HighlightColor

CRgbaColor m_CombinedPlacementColor

TModelUnit m_OverviewFactor

ratio to bar height

CRgbaColor m_ConcordantColor

TLabelPosition m_LabelPos

CRgbaColor m_DiscordantColor

TModelUnit m_BarHeight

absolute size (in pixel)

@ ePos_Side

always on 5' side

@ ePos_Above

above the rendered bar

CGlAttrGuard - guard class for restoring OpenGL attributes.

static string GetFeatSignature(const objects::CSeq_feat &feat, objects::CScope *scope, const string &data_source="", const string &sAdditionalInfo="")

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

void DrawArrowBoundary(TModelUnit x1, TModelUnit x2, TModelUnit x3, TModelUnit line_center, TModelUnit bar_h, TModelUnit head_h) const

TModelRange IntersectVisible(const CSeqGlyph *obj) const

void DrawArrow(TModelUnit x1, TModelUnit x2, TModelUnit x3, TModelUnit line_center, TModelUnit bar_h, TModelUnit head_h) const

void DrawRect(const TModelRect &rc) const

objects::CScope & GetScope()

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.

void x_InitHTMLActiveArea(CHTMLActiveArea &area) const

initialize the basic information for a given active area.

CRenderingContext * m_Context

the rendering context

virtual void SetHeight(TModelUnit h)

virtual TModelUnit GetRight() const

virtual void SetWidth(TModelUnit w)

virtual void SetLeft(TModelUnit l)

virtual TModelUnit GetTop() const

virtual TModelUnit GetHeight() const

virtual TModelUnit GetWidth() const

virtual TModelUnit GetLeft() const

TModelRect GetModelRect() const

get the bounding box.

vector< CHTMLActiveArea > TAreaVector

virtual TModelUnit GetBottom() const

Seq-loc iterator class – iterates all intervals from a seq-loc in the correct order.

CConstRef< CUser_field > GetFieldRef(const string &str, const string &delim=".", NStr::ECase use_case=NStr::eCase) const

bool HasField(const string &str, const string &delim=".", NStr::ECase use_case=NStr::eCase) const

Verify that a named field exists.

const CUser_field & GetField(const string &str, const string &delim=".", NStr::ECase use_case=NStr::eCase) const

Access a named field in this user object.

vector< TSeqRange > TIntervals

iterator_bool insert(const value_type &val)

static const int kHorzSpace

static const int kVertSpace

vertical space between elements.

GLubyte dense_vert_lines[]

GLubyte dense_diag_lines[]

GLubyte dense_horz_lines[]

GLubyte dense_vert_lines3[]

GLubyte dense_vert_lines2[]

unsigned int TSeqPos

Type for sequence locations and lengths.

#define ITERATE(Type, Var, Cont)

ITERATE macro to sequence through container elements.

virtual void Enable(GLenum glstate)=0

void Color3f(GLfloat r, GLfloat g, GLfloat b)

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 ShadeModel(GLenum mode)=0

Set shade model for default lighting: glShadeModel(GL_FLAT or GL_SMOOTH)

virtual void PolygonMode(GLenum face, GLenum mode)=0

Set the polygon rasterization mode.

virtual void PolygonStipple(GLubyte *mask)=0

Set polygon stipple pattern: glPolygonStipple(). Deprecated in gl 3.2+.

CGlRect< TModelUnit > TModelRect

virtual void Disable(GLenum glstate)=0

glDisable()

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.

static void GetLabel(const CObject &obj, string *label, ELabelType type=eDefault)

void SetLocation(const objects::CSeq_loc &loc)

string GetSeqIdString(bool with_version=false) const

Return seqid string with optional version for text seqid type.

bool Match(const CSeq_id &sid2) const

Match() - TRUE if SeqIds are equivalent.

ENa_strand GetStrand(void) const

Get the location's strand.

TRange GetTotalRange(void) const

bool IsSetStrand(void) const

Get strand.

bool IsSetStrand(EIsSetStrand flag=eIsSetStrand_Any) const

Check if strand is set for any/all part(s) of the seq-loc depending on the flag.

const CSeq_id * GetId(void) const

Get the id of the location return NULL if has multiple ids or no id at all.

TRange GetRange(void) const

Get the range.

ENa_strand GetStrand(void) const

TObjectType * GetPointer(void) const THROWS_NONE

Get pointer,.

TObjectType * GetPointer(void) THROWS_NONE

Get pointer,.

position_type GetLength(void) const

TThisType & CombineWith(const TThisType &r)

#define END_NCBI_SCOPE

End previously defined NCBI scope.

#define BEGIN_NCBI_SCOPE

Define ncbi namespace.

static const char label[]

TTo GetTo(void) const

Get the To member data.

TFrom GetFrom(void) const

Get the From member data.

const TStr & GetStr(void) const

Get the variant data.

const TData & GetData(void) const

Get the Data member data.

TBool GetBool(void) const

Get the variant data.

TConcordant GetConcordant(void) const

Get the Concordant member data.

bool CanGetClone_seq(void) const

Check if it is safe to call GetClone_seq method.

bool IsSetUnique(void) const

OPTIONAL? Check if a value has been assigned to Unique data member.

const TLocation & GetLocation(void) const

Get the Location member data.

bool IsSetConcordant(void) const

OPTIONAL? Check if a value has been assigned to Concordant data member.

bool CanGetSeq(void) const

Check if it is safe to call GetSeq method.

bool IsSetConfidence(void) const

Check if a value has been assigned to Confidence data member.

list< CRef< CClone_seq > > Tdata

TConfidence GetConfidence(void) const

Get the Confidence member data.

TSupport GetSupport(void) const

Get the Support member data.

bool IsSetPlacement_method(void) const

Check if a value has been assigned to Placement_method data member.

TUnique GetUnique(void) const

Get the Unique member data.

const Tdata & Get(void) const

Get the member data.

const TClone_seq & GetClone_seq(void) const

Get the Clone_seq member data.

TPlacement_method GetPlacement_method(void) const

Get the Placement_method member data.

const TSeq & GetSeq(void) const

Get the Seq member data.

bool CanGetSupport(void) const

Check if it is safe to call GetSupport method.

bool IsSetClone_seq(void) const

Check if a value has been assigned to Clone_seq data member.

@ eConfidence_multiple

Multiple hits.

@ eConfidence_virtual

Virtual (hasn't been sequenced)

@ eSupport_supporting

sequence supports placement

@ eSupport_supports_other

supports a different placement

@ eSupport_prototype

sequence used to place clone

@ eSupport_non_supporting

does not support any placement

@ ePlacement_method_end_seq_insert_alignment

combined end-seq and insert align

@ ePlacement_method_end_seq

Clone placed by end sequence.

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

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

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