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NCBI C++ ToolKit: src/gui/packages/pkg_snp/bins/bins_glyph.cpp Source File

& annot_name,

sprintf(buff,

,

, checksum, checksum_name);

objects::CScope * scope)

, m_bHasObjectList(

)

range = (*iNonEmptyBins)->obj->range;

TMappedBinList::const_iterator itNextBin = iNonEmptyBins;

((itNextBin !=

.end()) && (((*iNonEmptyBins)->SequentialNumber+1) == (*itNextBin)->SequentialNumber)) {

area.

= (*iNonEmptyBins)->obj->signature;

p_areas->push_back(area);

bin = (size_t) floor( (pos.

()-start)/window );

bin = max<size_t>(0, bin);

(

[bin].obj.Empty())

;

(iBin->obj.NotEmpty()) {

sColorKey(

);

(

bin = 0; bin < numBins; bin++)

(

[bin].obj.NotEmpty()) {

sColorBinKey =

;

sColorBinKey =

;

sColorBinKey =

;

sColorBinKey =

;

x1 = start + bin*(window);

x2 = start + (bin+1)*(window);

gl.

(.76f,.76f,.76f, 1.0f);

x1 = ((bin)*(window) + start);

dx = (isFlipped) ? 2 : -2;

x1+w, y2 - (binHeight - h) * 0.5,

);

x1+w, y2 - (binHeight - h) * 0.5,

);

gl.

(0.0f, 0.0f,0.0f, 1.0f);

static CRef< CScope > m_Scope

Checksum and hash calculation classes.

static string GenerateBinSignature(const string &title, const string &annot_name, TGi gi, TSeqRange range, objects::NSnpBins::TBinType BinType)

virtual void x_UpdateBoundingBox()

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

CConstRef< objects::CSeq_loc > m_Location

CBinsGlyph(const TDensityMap &values, const objects::CSeq_loc &loc, objects::CScope *scope)

TMappedBinList m_NonEmptyBins

virtual void x_Draw() const

The default renderer for this layout object.

virtual void GetHTMLActiveAreas(TAreaVector *p_areas) const

Get html active areas.

const string & GetTitle() const

TSeqRange x_GetBinRange(unsigned int bin) const

CRef< objects::CScope > m_Scope

const string & GetAnnotName() const

list< SBinMapped * > TMappedBinList

virtual TSeqRange GetRange(void) const

get the total range of this object.

virtual bool IsClickable() const

Query if this glyph is clickable.

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

Check if need to show tooltip.

virtual bool OnLeftDblClick(const TModelPoint &p)

void x_BuildNonEmptyBinList() const

objects::NSnpBins::TBinType m_Type

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

Get the tooltip if available.

string x_GetColorTheme() const

CConstRef< CSeqGraphicConfig > GetGlobalConfig() const

expose global configuration

CChecksum – Checksum calculator.

static CGuiRegistry & GetInstance()

access the application-wide singleton

@ fNoPin

tooltip is not pinnable

@ fNoSelection

the object can't be selected

int m_Flags

area flags, will need to replace m_Type

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

TVPUnit SeqToScreenXClipped(const TModelUnit &size) const

void DrawRect(const TModelRect &rc) const

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

const TModelUnit & GetScale() const

bool IsFlippedStrand() 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 void SetHeight(TModelUnit h)

const CRenderingContext * GetRenderingContext() const

Get the rendering context.

virtual void SetWidth(TModelUnit w)

virtual void SetLeft(TModelUnit l)

virtual TModelUnit GetTop() const

vector< CHTMLActiveArea > TAreaVector

const CSeqGlyph * GetParent(void) const

const string & GetColorTheme() const

objects and functions for dealing with variation (historically called SNP) bins

@ eIND

individual tracks (Venter, Watson, etc), data same as in eCLIN

@ eCITED

Cited Variations.

@ eCLIN

Clinical Variations.

@ eGAP

dbGaP analysis files

@ eGCAT

NHGRI GWAS Catalog Track (AKA Association Results)

unsigned int TSeqPos

Type for sequence locations and lengths.

#define ITERATE(Type, Var, Cont)

ITERATE macro to sequence through container elements.

#define NON_CONST_ITERATE(Type, Var, Cont)

Non constant version of ITERATE macro.

void AddLine(const char *line, size_t len)

Uint4 GetChecksum(void) const

Return calculated checksum.

IRender & GetGl()

convenience function for getting current render manager

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

void Color4f(GLfloat r, GLfloat g, GLfloat b, GLfloat a)

void SetHorz(T left, T right)

virtual void ColorC(const CRgbaColor &c)=0

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

@ eFontFace_Helvetica_Bold

CRgbaColor ContrastingColor(bool onlyBW=true) const

Return a color guaranteed to contrast nicely with this color.

static const int c_BinWidth

standard width and height of a bin

static string PValueAsColorKey(double pvalue)

preferred colorings for a given pvalue

static string ClinSigAsColorKey(NSnp::TClinSigID ClinSigID)

preferred colorings for SNP clinical significances

virtual bool IsEmpty() const =0

Indicates if the tooltip is empty.

static void GetBinTooltip(const NSnpBins::SBin &bin, CIRef< ITooltipFormatter > pFormatter, TGi gi, const std::string &colorTheme)

generate a tooltip for a given bin object and put it into the formatter

static const int c_BinHeight

TGi GetGiForId(const objects::CSeq_id &id, CScope &scope, EGetIdType flags=0)

Given a Seq-id retrieve the corresponding GI.

uint32_t Uint4

4-byte (32-bit) unsigned integer

uint16_t Uint2

2-byte (16-bit) unsigned integer

position_type GetLength(void) const

#define END_NCBI_SCOPE

End previously defined NCBI scope.

#define BEGIN_NCBI_SCOPE

Define ncbi namespace.

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

Convert int to string.

TTo GetTo(void) const

Get the To member data.

TFrom GetFrom(void) const

Get the From member data.

static void text(MDB_val *v)

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