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NCBI C++ ToolKit: src/gui/widgets/aln_multiple/trace_graph.cpp Source File

: m_SignalStyle(eCurve),

m_ConfGraphState(eExpanded),

m_SignalGraphState(eExpanded),

m_bReverseColors(

)

: m_DataProxy(handle, b_neg_strand),

m_TextColor(0.6f, 0.6f, 0.6f)

v = 1.0f - k * j;

}

;

AttrGuard(GL_ENABLE_BIT | GL_COLOR_BUFFER_BIT | GL_HINT_BIT

| GL_LINE_SMOOTH | GL_POLYGON_MODE | GL_LINE_BIT);

unique_ptr<IAlnSegmentIterator> it_1(it.

());

gl.

(GL_SRC_ALPHA, GL_ONE_MINUS_SRC_ALPHA);

gl.

(GL_LINE_SMOOTH);

glHint(GL_LINE_SMOOTH_HINT, GL_NICEST);

unique_ptr<IAlnSegmentIterator> it_3(it.

());

unique_ptr<IAlnSegmentIterator> it_4(it.

());

unique_ptr<IAlnSegmentIterator> it_2(it.

());

gl.

(x1, y1, x2, y2);

gl.

(x1, y3, x2, y4);

= 0.000001f;

b_average = (scale_x > 0.3);

gl.

(GL_LINES);

it_seg_moved =

;

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

(

pix = range_pix_start;

pix <= range_pix_end && it_seg && pos <= gr_to; ) {

b_first =

;

to =

(ch_range.

(), gr_to);

(vis_to < vis_from) {

(vis_from, vis_to);

from =

(from, vis_from);

to =

(to, vis_to);

it_seg_moved =

;

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

pos_pix_right = pos_pix_left + 1 / scale_x;

(pos >= from && pos <= to && pos_pix_left < pix + 1) {

v_min = b_first ? v :

(v_min, v);

v_max = b_first ? v :

(v_max, v);

(pos_pix_right < pix +1) {

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

pos_pix_right = pos_pix_left + 1 / scale_x;

(ch_pix_end < pix + 1) {

it_seg_moved =

;

gl.

(0.0f, 0.5f, 0.0f);

gl.

(0.0f, 0.75f, 0.25f);

v = v_min = v_max = 0;

gl.

(0.0f, 0.5f, 0.0f);

( ; it_seg; ++it_seg ) {

x = aln_pos - offset_x;

gl.

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

(

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

unique_ptr<IAlnSegmentIterator> p_it_1(it.

());

(it_1->IsAligned()) {

bottom_y,

,

amp)

(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_QUAD_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));

gl.

(aln_from - offset_x, bottom_y - v);

(

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

v = values[i_sm];

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));

gl.

(aln_to - offset_x, bottom_y - v);

v = values[sm_end];

gl.

(aln_pos - offset_x, bottom_y - v);

band_h = av_h / 4;

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

gl.

(GL_LINES);

(

pix = range_pix_start; pix <= range_pix_end && it_seg; ++it_seg) {

(vis_to < vis_from) {

(vis_from, vis_to);

from =

(from, vis_from);

to =

(to, vis_to);

sm_start =

(sm_start, 0);

(aln_from, aln_to);

pix_start = range_pix_start + (

) floor((aln_from - left) / scale_x);

pix_end = range_pix_start + (

) ceil((aln_to - left) / 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];

v1 =

= values[sample];

(pix_x1 < pix + 1) {

b_next_point =

->

() ? (sample > sm_start) : (sample < sm_end);

x2 = positions[sample + sm_inc];

= 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;

b_next_point =

->

() ? (sample > sm_start) : (sample < sm_end);

x2 = positions[sample + sm_inc];

= 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.

class CRgbaColor provides a simple abstraction for managing colors.

TSignedSeqPos GetSeqFrom() const

Sequence related information.

TConfidence GetConfidence(TSignedSeqPos pos) const

TSignalValue GetMax(EChannel signal) const

int GetSamplesCount() const

TValues & GetValues(EChannel signal)

TConfidence GetMaxConfidence() const

TSignedSeqPos GetSeqTo() const

TPositions & GetPositions()

vector< TFloatSeqPos > TPositions

vector< TSignalValue > TValues

TSignedSeqPos GetSeqLength() const

EGraphState m_ConfGraphState

ESingnalStyle m_SignalStyle

EGraphState m_SignalGraphState

CTraceGraphProperties & operator=(const CTraceGraphProperties &orig)

void x_RenderIntensityGraphs(CGlPane &pane, int y, int h, IAlnSegmentIterator &it)

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

void x_RenderText(CGlPane &pane)

void x_RenderSignalGraph(CGlPane &pane, int y, int h, IAlnSegmentIterator &it)

vector< CRgbaColor > m_vSignalColors

CTraceGraph(const objects::CBioseq_Handle &handle, bool b_neg_strand)

CTraceDataProxy m_DataProxy

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...

virtual void Render(CGlPane &pane)

void x_RenderContour(CGlPane &pane, int y, int conf_h, int total_h, IAlnSegmentIterator &it)

void SetSignalGraphState(EGraphState state)

void x_RenderCurveSegment(CGlPane &pane, const IAlnSegment &seg, const CTraceData::TPositions &positions, const CTraceData::TValues &values, int bottom_y, int h, int amp)

void SetConfGraphState(EGraphState state)

virtual bool IsCreated() const

Graph is not considered fully functional until it has been "created" by the call to create function.

void x_RenderConfGraph(CGlPane &pane, int y, int h, IAlnSegmentIterator &it)

int x_GetConfGraphH() const

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

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

int x_GetSignalGraphH() const

virtual string GetTooltip()

virtual const IAlnRowGraphProperties * GetProperties() const

virtual void SetProperties(IAlnRowGraphProperties *props)

int x_FindSampleToLeft(double pos) const

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

CTraceGraphProperties m_Props

virtual TVPPoint PreferredSize()

Alignment segment iterator interface.

virtual IAlnSegmentIterator * Clone(void) const =0

Create a copy of the iterator.

Alignment segment interface.

virtual const TSignedRange & GetRange(void) const =0

Get the selected row range.

bool IsAligned(void) const

virtual const TSignedRange & GetAlnRange(void) const =0

Get alignment range for the segment.

Include a standard set of the NCBI C++ Toolkit most basic headers.

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)

virtual void Enable(GLenum glstate)=0

virtual void Begin(GLenum mode)=0

Start rendering.

CGlPoint< TVPUnit > TVPPoint

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)

TModelUnit GetOffsetY() const

bool PtInRect(T x, T y) const

virtual void End()=0

Finish rendering (create buffer and send to renderer)

void Inflate(T d_x, T d_y)

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

Set the polygon rasterization mode.

EProjectionMode GetProjMode(void) const

virtual void TextOut(const char *text) const

TextOut interface Write the specified text and set up state and transformation as needed.

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)

position_type GetLength(void) const

TThisType & IntersectWith(const TThisType &r)

bool NotEmpty(void) const

CRange< TSignedSeqPos > TSignedSeqRange

#define END_NCBI_SCOPE

End previously defined NCBI scope.

#define BEGIN_NCBI_SCOPE

Define ncbi namespace.

TTo GetTo(void) const

Get the To member data.

TFrom GetFrom(void) const

Get the From member data.

unsigned int

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

where boath are integers</td > n< td ></td > n</tr > n< tr > n< td > tse</td > n< td > optional</td > n< td > String</td > n< td class=\"description\"> TSE option controls what blob is orig

const GenericPointer< typename T::ValueType > T2 value

const TSignedSeqRange * m_AlnRange

double GetSeqPosFromAlnPos(double aln_pos)

double GetAlnPosFromSeqPos(double seq_pos)

const TSignedSeqRange * m_SeqRange

void Init(const TSignedSeqRange &seq_range, const TSignedSeqRange &aln_range, bool negative)

TSignedSeqPos GetAlnPosFromSeqPos(TSignedSeqPos seq_pos)

TSignedSeqPos GetSeqPosFromAlnPos(TSignedSeqPos aln_pos)

static const int kSignalGraphPrefH

static const int kGradColors

CTraceGraph.

static const int kGraphOffsetY

static const int kTextOff

static const int kIntBandSpace

static const int kCollapsedGraphH

static const int kConfGraphPrefH

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