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Showing content from http://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/doxyhtml/seq__text_2seq__graph_8cpp_source.html below:

NCBI C++ ToolKit: src/gui/widgets/seq_text/seq_graph.cpp Source File

51

m_BackColor(0.9f, 0.9f, 0.9f),

52

m_TextColor(0.0f, 0.0f, 0.0f),

53

m_FeatColor(0.0f, 0.6f, 0.0f),

54

m_SpliceBoxColor(0.5f, 0.5f, 0.5f),

119 for

(

= seq_start;

< seq_start + num_chars_per_row;

++) {

120 if

(splice_sites [

]) {

121

x1 = offset_X +

- seq_start - 0.5;

122

x2 = offset_X +

- seq_start + 0.5;

125

gl.

Begin

(GL_LINES);

152 for

(

= seq_start;

< subtypes.size() &&

- seq_start < num_chars_per_row;

++) {

173 for

(

= 0;

< breaks.size();

++) {

174 if

(breaks[

] >= seq_start && breaks[

] <= seq_start + num_chars_per_row) {

176

gl.

Begin

(GL_LINES);

177

gl.

Vertex2d

(x + breaks[

] - seq_start - 0.5, y);

196 unsigned int

first_var = 0,

;

204 for

(

= 0;

< variations.size();

++) {

205 for

(

unsigned int

k =

+ 1;

206

k < variations.size() && variations[k].GetFeatLeft() < variations[

].GetFeatLeft() + variations[

].GetDrawWidth();

208

variations[k].SetDisplayLine(

max

(variations[

].GetDisplayLine() + 1, variations[k].GetDisplayLine()));

212 while

(first_var < variations.size() && variations[first_var].GetFeatRight() < seq_start) {

216 if

(first_var == variations.size()) {

223 colors

.push_back (variation_color);

224 colors

.push_back (variation_color);

225 colors

.push_back (variation_color);

226 colors

.push_back (variation_color);

227 colors

.push_back (variation_color);

229 while

(first_var < variations.size() && variations[first_var].GetFeatLeft() < seq_start + num_chars_per_row) {

230 TSeqPos

varlinestart =

max

(seq_start, variations[first_var].GetFeatLeft());

231 TSeqPos

varlinestop =

min

(seq_start + num_chars_per_row - 1,

232

variations[first_var].GetFeatLeft() + variations[first_var].GetDrawWidth());

233 if

(varlinestart <= varlinestop) {

237

seq_left.

m_Y

-= variations[first_var].GetDisplayLine();

238

seq_right.

m_Y

-= variations[first_var].GetDisplayLine();

242 if

(varlinestart > variations[first_var].GetFeatLeft()) {

243

var_start = varlinestart - variations[first_var].GetFeatLeft();

246 while

(

colors

.size() < varlinestop - varlinestart + 1) {

247 colors

.push_back (variation_color);

250

variations[first_var].GetText().substr(var_start, varlinestop - varlinestart + 1).c_str(),

268 TSeqPos

chars_in_line, lines_in_seq;

270 if

(chars_in_line < 1) {

277 if

(scale_x < 0)

return

;

300 colors

.reserve(chars_in_line);

312 bool

color_exons_for_mrna =

true

;

316

subtypes.reserve((vis_stop - vis_start) + 1);

317

splice_sites.reserve((vis_stop - vis_start) + 1);

327

color_exons_for_mrna =

false

;

330

color_exons_for_mrna =

false

;

334 if

(color_exons_for_mrna) {

348 while

(row_start < vis_stop && row_start <

len

)

351

start_point.

m_X

+= 0.5;

354 x_BoxCharacters

(splice_sites, row_start - vis_start, chars_in_line, start_point.

m_X

, start_point.

m_Y

);

363

substr = seq.substr (row_start - vis_start, chars_in_line);

365

substr.c_str(), &

colors

366

(

float

) scale_x, (

float

) scale_y);

369 x_DrawVariations

(row_start, chars_in_line, (

float

) scale_x, (

float

) scale_y, variations);

371

row_start += chars_in_line;

394 return "No sequence loaded"

;

class CRgbaColor provides a simple abstraction for managing colors.

@ eSubtype_bad

These no longer need to match the FEATDEF values in the C toolkit's objfdef.h.

bool GetShowFeatAsLower()

CRgbaColor * GetColor(int subtype) const

objects::SAnnotSelector * GetCaseFeature()

CSeqTextPaneConfig::EFeatureDisplayType GetFeatureColorationChoice()

CSeqTextDataSource implements Adapter design pattern.

void GetSeqData(TSeqPos start, TSeqPos stop, string &buffer, objects::SAnnotSelector *feat_sel=NULL, bool showFeatAsLower=false)

void GetFeatureData(TSeqPos start_offset, TSeqPos stop_offset, CSeqTextConfig *cfg, ISeqTextGeometry *pParent, CSeqTextDefs::TSubtypeVector &subtypes, CSeqTextDefs::TSpliceSiteVector &splice_sites, CSeqTextDefs::TVariationGraphVector &variations)

void GetIntervalBreaks(TSeqPos start_offset, TSeqPos stop_offset, CSeqTextDefs::TSeqPosVector &breaks)

void GetSubtypesForAlternatingExons(TSeqPos start_offset, TSeqPos stop_offset, ISeqTextGeometry *pParent, CSeqTextDefs::TSubtypeVector &subtypes)

vector< CSeqTextVariationGraph > TVariationGraphVector

vector< bool > TSpliceSiteVector

vector< int > TSubtypeVector

vector< TSeqPos > TSeqPosVector

ISequenceTextGraphHost * m_pHost

virtual TVPPoint PreferredSize()

virtual void Render(CGlPane &pane)

void SetFont(CGlTextureFont *seq_font)

void x_GetColors(CSeqTextDefs::TSubtypeVector &subtypes, TColorVector &colors, TSeqPos seq_start, TSeqPos num_chars_per_row)

vector< CRgbaColor * > TColorVector

void x_BoxCharacters(ncbi::CSeqTextDefs::TSpliceSiteVector splice_sites, TSeqPos seq_start, TSeqPos num_chars_per_row, TModelUnit offset_X, TModelUnit offset_Y)

virtual void SetModelRect(const TModelRect &rc)

virtual bool NeedTooltip(CGlPane &pane, int vp_x, int vp_y)

void x_RenderSequence(CGlPane &pane)

void SetGeometry(ISeqTextGeometry *pGeometry)

virtual void SetDataSource(CSeqTextDataSource *p_ds)

void SetConfig(CSeqTextConfig *p_cfg)

CRef< CSeqTextConfig > m_Config

virtual TModelRect GetModelRect() const

void x_DrawVariations(TSeqPos seq_start, TSeqPos num_chars_per_row, float scale_x, float scale_y, CSeqTextDefs::TVariationGraphVector &variations)

ISeqTextGeometry * m_pGeometry

void x_DrawIntervalBreaks(TModelUnit x, TModelUnit y, CSeqTextDefs::TSeqPosVector &breaks, TSeqPos seq_start, TSeqPos num_chars_per_row)

CRef< CGlTextureFont > m_pSeqFont

virtual string GetTooltip()

CRgbaColor m_SpliceBoxColor

CRef< CSeqTextDataSource > m_DataSource

void SetHost(ISequenceTextGraphHost *pHost)

virtual void STG_GetVisibleRange(TSeqPos &seq_start, TSeqPos &seq_stop)=0

virtual TModelPoint STG_GetModelPointBySourcePos(TSeqPos z)=0

virtual void STG_GetLineInfo(TSeqPos &chars_in_line, TSeqPos &lines_in_pane)=0

class ISequenceTextGraphHost

virtual void STGH_GetMouseOverFeatureSubtypes(CSeqTextDefs::TSubtypeVector &subtypes)=0

virtual void STGH_GetSelectedFeatureSubtypes(CSeqTextDefs::TSubtypeVector &subtypes)=0

static const Colors colors

unsigned int TSeqPos

Type for sequence locations and lengths.

virtual void Begin(GLenum mode)=0

Start rendering.

IRender & GetGl()

convenience function for getting current render manager

void Vertex2d(GLdouble x, GLdouble y)

void ArrayTextOut(TModelUnit x, TModelUnit y, TModelUnit dx, TModelUnit dy, const char *text, const vector< CRgbaColor * > *colors=NULL, TModelUnit scale_x=1.0f, TModelUnit scale_y=1.0f) const

prints array of characters in positions (x + i*dx, y + i*dy) where "i" is index of a character in the...

bool PtInRect(T x, T y) const

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.

virtual TModelUnit GetMetric(EMetric metric, const char *text=NULL, int len=-1) const

virtual void LineWidth(GLfloat w)=0

Set line width for drawing: glLineWidth()

TModelUnit GetScaleX(void) const

TModelUnit GetScaleY(void) const

virtual void ColorC(const CRgbaColor &c)=0

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

#define END_NCBI_SCOPE

End previously defined NCBI scope.

#define BEGIN_NCBI_SCOPE

Define ncbi namespace.

unsigned int

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

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

The NCBI C++/STL use hints.

static const int kTextOffset

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