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

, m_ShowTitle(

)

(

ch = 0; ch < 4; ++ch) {

tt.

(

);

AttrGuard(GL_ENABLE_BIT | GL_COLOR_BUFFER_BIT | GL_HINT_BIT

| GL_LINE_SMOOTH | GL_POLYGON_MODE | GL_LINE_BIT);

top_y = m_ModelRect.

();

gl.

(GL_SRC_ALPHA, GL_ONE_MINUS_SRC_ALPHA);

gl.

(GL_LINE_SMOOTH);

glHint(GL_LINE_SMOOTH_HINT, GL_NICEST);

gl.

(x1, y1, x2, y2);

gl.

(x1, y3, x2, y4);

b_average = (scale_x > 0.5);

v = 0, v_min = 0, v_max = 0;

(vis_from > vis_to) {

(vis_from, vis_to);

gl.

(GL_LINES);

(

pix = range_pix_start; pix <= range_pix_end;) {

(pos < gr_from || pos > gr_to)

b_first =

;

pos_pix_left = range_pix_start + (left - pos) / scale_x;

pos_pix_left = range_pix_start + (pos - left) / scale_x;

pos_pix_right = pos_pix_left + 1 / scale_x;

(pos_pix_left < pix + 1) {

(pos < from || pos > to)

v_min =

(v_min, v);

v_max =

(v_max, v);

(pos_pix_right >= pix + 1)

pos_pix_left = range_pix_start + (left - pos) / scale_x;

pos_pix_left = range_pix_start + (pos - left) / scale_x;

pos_pix_right = pos_pix_left + 1 / scale_x;

v = v_min = v_max = 0;

from = max<TSignedSeqPos>(gr_from, from);

to = min<TSignedSeqPos>(gr_to, to);

x = aln_pos - offset_x;

gl.

(x, base_y, x + 1.0, base_y + v);

(

i_ch = 0; i_ch < 4; i_ch++) {

bottom_y,

,

amp)

vis_from = rc_vis.

();

vis_to = rc_vis.

();

(vis_to < vis_from) {

(vis_from, vis_to);

from =

(from, vis_from);

to =

(to, vis_to);

sm_start =

(0, sm_start);

(sm_start <= sm_end) {

gl.

(GL_TRIANGLE_STRIP);

(sm_start_seqpos < from) {

(sm_start + 1 < sm_end) {

v1 = values[sm_start];

= values[sm_start + 1];

x1 = sm_start_seqpos;

x2 = positions[sm_start + 1];

v = v1 + ((from - x1) * (

- v1) / (x2 - x1));

aln_from = from + (b_neg ? -1 : 0);

gl.

(aln_from - offset_x, bottom_y - v);

(

i_sm = sm_start; i_sm < sm_end; i_sm++) {

v = values[i_sm];

aln_pos = seqpos + (b_neg ? -1 : 0);

gl.

(aln_pos - offset_x, bottom_y - v);

(sm_end - 1 > sm_start) {

v1 = values[sm_end - 1];

= values[sm_end];

x1 = positions[sm_end - 1];

x2 = positions[sm_end];

v = v1 + ((to + 1 - x1) * (

- v1) / (x2 - x1));

aln_to = to + (b_neg ? 0 : 1);

gl.

(aln_to - offset_x, bottom_y - v);

v = values[sm_end];

aln_pos = seqpos;

gl.

(aln_pos - offset_x, bottom_y - v);

band_h = av_h / 4;

off = (av_h - 4 * band_h) / 2;

gl.

(GL_LINES);

vis_from = rc_vis.

();

vis_to = rc_vis.

();

(vis_to < vis_from) {

(vis_from, vis_to);

sm_start =

(sm_start, 0);

aln_from = from;

pix_start = range_pix_start + (aln_from - floor(vis_from)) / scale_x;;

pix_end = range_pix_start + (

)ceil((aln_to - floor(vis_from)) / scale_x);

pix_start =

(pix_start, range_pix_start);

pix_end =

(pix_end, range_pix_end);

(

i_ch = 0; i_ch < 4; i_ch++) {

x1 = 0.0, x2 = 0.0, pix_x1 = 0.0, pix_x2 = 0.0;

v1,

, s, dx, sum, sum_pix_x;

(

pix = pix_start; pix <= pix_end; pix++) {

x1 = positions[sample];

pix_x1 = range_pix_start;

pix_x1 += dist / scale_x;

v1 =

= values[sample];

(pix_x1 < pix + 1) {

x2 = positions[sample + sm_inc];

pix_x2 = range_pix_start;

pix_x2 += dist / scale_x;

= values[sample + sm_inc];

v1 += (

- v1) * (pix - pix_x1) / (pix_x2 - pix_x1);

(b_next_point && pix_x2 <= pix + 1)

dx = pix_x2 - pix_x1;

s = 0.5 * (v1 +

) * dx;

x2 = positions[sample + sm_inc];

pix_x2 = range_pix_start;

pix_x2 += dist / scale_x;

= values[sample + sm_inc];

(b_next_point && pix_x2 > pix + 1) {

dx = pix + 1 - pix_x1;

v = v1 + (

- v1) * dx / (pix_x2 - pix_x1);

s = 0.5 * (v1 + v) * dx;

av_v = (sum_pix_x) > 0 ? sum / sum_pix_x : 0;

norm = (MaxSignal == 0) ? 0 : (av_v / MaxSignal);

gl.

(pix, band_y + band_h - 1);

(signal >= 0 && signal <= 3);

(pos < m_Data->GetSeqFrom() || n_samples == 0) {

=

(

, n_samples - 1);

(positions[

] > pos) {

(;

> 0 && positions[

] > pos;

--) {

(; ++

< n_samples && positions[

] < pos;) {

(pos < m_Data->GetSeqFrom() || n_samples == 0) {

=

(

, n_samples - 1);

(positions[

] > pos) {

(;

> 0 && positions[

] > pos;

--) {

(; ++

< n_samples && positions[

] < pos;) {

CGlAttrGuard - guard class for restoring OpenGL attributes.

CGlPane * GetGlPane()

inline method implementations

const TModelRange & GetVisibleRange() const

bool IsFlippedStrand() const

class CRgbaColor provides a simple abstraction for managing colors.

TValues & GetValues(EChannel signal)

int GetSamplesCount() const

vector< TSignalValue > TValues

vector< TFloatSeqPos > TPositions

TConfidence GetMaxConfidence() const

TSignedSeqPos GetSeqTo() const

TSignedSeqPos GetSeqFrom() const

Sequence related information.

TPositions & GetPositions()

TSignalValue GetMax(EChannel signal) const

TConfidence GetConfidence(TSignedSeqPos pos) const

TSignedSeqPos GetSeqLength() const

CRenderingContext * m_Context

the rendering context

virtual void SetHeight(TModelUnit h)

virtual void SetWidth(TModelUnit w)

virtual void SetLeft(TModelUnit l)

virtual TModelUnit GetHeight() const

TModelRect GetModelRect() const

get the bounding box.

vector< CHTMLActiveArea > TAreaVector

int x_GetConfGraphH() const

virtual bool OnLeftDblClick(const TModelPoint &)

vector< CRgbaColor > m_vSignalColors

void x_RenderConfGraph(CGlPane &pane, int y, int h) const

void x_RenderSignalGraph(CGlPane &pane, int y, int h) const

int x_FindSampleToLeft(double pos) const

returns index of rightmost sample having m_SeqPos less then "pos".

CTraceGlyph(const CRef< CSGTraceData > &data, const CRef< CTraceGraphConfig > &config)

virtual bool IsClickable() const

Query if this glyph is clickable.

CRef< CTraceGraphConfig > m_Config

void x_InitColors() const

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

Get the tooltip if available.

virtual void GetHTMLActiveAreas(TAreaVector *p_areas) const

Get html active areas.

CRef< CSGTraceData > m_Data

void x_RenderCurveSegment(CGlPane &pane, const CSGTraceData::TPositions &positions, const CSGTraceData::TValues &values, int bottom_y, int, int amp) const

const CRgbaColor & GetColorByValue(double value, int signal) const

void x_RenderIntensityGraphs(CGlPane &pane, int y, int h) const

Render signals for all channels as gradient-color bands with color intensity proprotional to signal s...

int x_FindSampleToRight(double pos) const

returns index of the leftmost sample having m_SeqPos greater than "pos" if "pos" is to the left of th...

void x_RenderContour(CGlPane &pane, int y, int top_h, int total_h) const

virtual void x_Draw() const

The default renderer for this layout object.

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

Check if need to show tooltip.

int x_GetSignalGraphH() const

virtual void x_UpdateBoundingBox()

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

ESingnalStyle m_SignalStyle

CRgbaColor m_colorConfMax

EGraphState m_ConfGraphState

EGraphState m_SignalGraphState

array< CRgbaColor, 4 > m_colors

CRgbaColor m_colorConfMin

int TSignedSeqPos

Type for signed sequence position.

void swap(NCBI_NS_NCBI::pair_base_member< T1, T2 > &pair1, NCBI_NS_NCBI::pair_base_member< T1, T2 > &pair2)

void SetViewport(const TVPRect &R)

virtual void Enable(GLenum glstate)=0

virtual void Begin(GLenum mode)=0

Start rendering.

virtual void BlendFunc(GLenum sfactor, GLenum dfactor)=0

Options to be used when GL_BLEND is enabled.

void Color3d(GLdouble r, GLdouble g, GLdouble b)

IRender & GetGl()

convenience function for getting current render manager

void Vertex2d(GLdouble x, GLdouble y)

TVPRect & GetViewport(void)

virtual void End()=0

Finish rendering (create buffer and send to renderer)

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

Set the polygon rasterization mode.

EProjectionMode GetProjMode(void) const

TModelRect & GetVisibleRect(void)

virtual void Disable(GLenum glstate)=0

glDisable()

virtual void LineWidth(GLfloat w)=0

Set line width for drawing: glLineWidth()

TModelUnit GetScaleX(void) const

TModelUnit GetOffsetX() const

virtual void ColorC(const CRgbaColor &c)=0

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

void Rectd(GLdouble x1, GLdouble y1, GLdouble x2, GLdouble y2)

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

add a row with a cell, spanning across all columns

static void RgbToHsv(const CRgbaColor &rgb, float &h, float &s, float &v)

convert RGB to HSV.

static CRgbaColor HsvToRgb(float h, float s, float v)

position_type GetLength(void) const

#define END_NCBI_SCOPE

End previously defined NCBI scope.

#define BEGIN_NCBI_SCOPE

Define ncbi namespace.

TFrom GetFrom(void) const

Get the From member data.

unsigned int

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

const GenericPointer< typename T::ValueType > T2 value

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

static const double kSignalGraphPrefHR

CRgbaColor s_GradientToWhite(const CRgbaColor &rgb, float degree)

static const int kGradColors

static const double kConfGraphPrefHR

static const int kGraphOffsetY

static const int kCollapsedGraphH

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