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

, m_SeqAlign(&mapped_align)

, m_OrigSeqAlign(orig_align)

, m_OrigAnchor(orig_anchor)

, m_ShowScore(

)

, m_DisableTooltipsCaching(

)

CreateObjectInterface<IGuiObjectInfo>(scoped_obj,

));

( !gui_info )

;

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

gui_info->GetLinks(tt,

);

tt.

(

);

tt.

(

);

tt.

(

);

p_areas->push_back(area);

(

.seq_range.Empty())

(

= 0;

< row_num; ++

) {

(

== anchor) {

unique_ptr<IAlnSegmentIterator> p_it(

.base_width_anchor;

.base_width_anchor;

(curr_seq_from > curr_seq_to) {

(curr_seq_from, curr_seq_to);

curr_seq_to += 1.0 /

.base_width_anchor;

(gap_size > 1.5) {

(

.seq_range.Empty())

(

= 0;

< row_num; ++

) {

(

== anchor) {

unique_ptr<IAlnSegmentIterator> p_it(

last_aligned_seg_to_anchor = -2;

last_aligned_seg_to_curr = -2;

last_aligned_seg_from_anchor = -2;

last_aligned_seg_from_curr = -2;

last_large_ins = -100000;

seg_iter_dir = 0;

(seg_iter_dir == 0) {

(last_aligned_seg_to_anchor < 0) {

last_aligned_seg_to_anchor = anchor_to;

last_aligned_seg_from_anchor = anchor_from;

(anchor_to < last_aligned_seg_to_anchor || anchor_from < last_aligned_seg_to_anchor) {

(seg_iter_dir == -1) {

((

)t_pos == last_aligned_seg_from_anchor - 1) {

start = t_pos /

.base_width_anchor;

(

.reverse_strand) {

ins_len = last_aligned_seg_from_curr - seg.

().

();

last_aligned_seg_to_anchor = t_pos;

}

(seg_iter_dir == 1) {

((

)f_pos == last_aligned_seg_to_anchor + 1) {

start = f_pos /

.base_width_anchor;

(

.reverse_strand) {

ins_len = last_aligned_seg_from_curr - seg.

().

();

last_aligned_seg_from_anchor = f_pos;

start /=

.base_width_anchor;

last_aligned_seg_to_anchor = -2;

last_aligned_seg_from_anchor = -2;

(ins_len <= 0)

;

ins_len_pix /=

.base_width_anchor;

}

(ins_len_pix > 2.0) {

last_large_ins = (

)start;

(ins_len_pix < 0.1f)

start + size_in_model,

.yy - over,

start - size_in_model,

.yy - over);

start - size_in_model,

.yy +

.bar_h + over,

start + size_in_model,

.yy +

.bar_h + over);

(unaligned_regions.begin(), unaligned_regions.end(),

return a.GetFrom() < b.GetFrom();

(unaligned_regions.empty()) {

(

& unaligned_rng : unaligned_regions) {

ln_start = unaligned_rng.GetToOpen();

(

.seq_range.Empty())

(aln_range.

() > 0) {

(

= 0;

< row_num; ++

) {

(

== anchor) {

unique_ptr<IAlnSegmentIterator> p_it(

.base_width_anchor;

.base_width_anchor;

(curr_seq_from > curr_seq_to) {

(curr_seq_from, curr_seq_to);

curr_seq(curr_seq_from, curr_seq_to - 1);

(visible_range.

())

unaligned_regions.emplace_back(visible_range.

() + 1, visible_range.

() + 1);

(h_text >

.bar_h) {

sLabelTextOut +=

;

labelsCount =

(visible_range.

() / seg_width);

((label_width + label_width*0.5) >= visible_range.

()) {

xLF = visible_range.

();

(

= 0;

< labelsCount; ++

) {

xM = visible_range.

() + part_size / 2.0 +

*part_size;

xLT = visible_range.

() + part_size / 2.0 +

*part_size - half_label;

->

(&l_font, sLabelTextOut.c_str(), xM, yM,

,

);

xLF = visible_range.

() + part_size / 2.0 +

*part_size + half_label;

(

.bar_h <= 2)

(tail_5 >

.tail_5)

tail_5 -=

.tail_5;

(tail_3 >

.tail_3)

tail_3 -=

.tail_3;

(h_text <

.bar_h) {

(h_text <

.bar_h) {

(

.tail_5 > 0) {

(

.tail_3 > 0) {

((tail_5 >

.tail_5) || (tail_3 >

.tail_3))

(!visible_range.

()) {

aligned_seq = anchor == 0 ? 1 : 0;

visible_unaligned_range(range);

(inrc.

()) {

ab = mhndl.

();

rb = hndl.

();

(

.reverse_strand) {

translated_seq;

translated_seq = seq;

(

bp = 0; bp < seq.size(); bp++) {

pos = sStart + bp + addon;

pos = sStart + bp * 3 + addon + 1;

(

.seq_range.Empty())

( !splice5.empty() && !splice3.empty() &&

pre_stop = neg_genomic ?

(

.seq_range.Empty())

(

.override_color)

c =

.read_status_color;

(

.override_color)

xM = (

.whole_range.GetFrom() +

.whole_range.GetTo()) * 0.5;

identity = 100.0;

identities = (

)align_length;

identity = identities * 100 / align_length;

(identity > 0.6) {

identity = 1.75 * identity - 0.75;

(

.override_color)

(aligned_seq < 0) {

.f /=

.base_width_anchor;

.t /=

.base_width_anchor;

.whole_range =

.seq_range;

(

.seq_range.Empty()) {

<<

);

.override_color =

;

.half =

.bar_h * 0.5;

(aln_r_s > aln_r_e) {

(aln_r_s, aln_r_e);

(show_unaligned_tails) {

show_unaligned_tails =

;

(

.reverse_strand) {

(

.reverse_strand && !(show_unaligned_tails &&

.tail_5)) {

.f - over2,

.yy - 1,

.f - over2,

.yy +

.bar_h + 1);

(!(show_unaligned_tails &&

.tail_3)) {

.t + 1 + over2,

.yy - 1,

.t + 1 + over2,

.yy +

.bar_h + 1);

(

= 0;

< row_num; ++

) {

(

== anchor) {

(

->IsAverageable()) {

.override_color,

.read_status_color);

.override_color,

.read_status_color);

(show_unaligned_tails) {

(

.tail_5 > 0) {

(

.tail_3 > 0) {

*title =

+

(title->length() > 20 && title->find(

) != string::npos) {

pos = title->find_last_of(

);

(pos != string::npos) {

*title = title->substr(pos + 1);

(title->length() > 20) {

pos = title->rfind(

);

(pos != string::npos && pos > 0) {

pos = title->rfind(

, pos - 1);

(pos != string::npos) {

*title = title->substr(pos + 1);

gl.

(GL_SRC_ALPHA, GL_ONE_MINUS_SRC_ALPHA);

tail_len =

(tail_5, visible_tail_5, base_width_curr);

tail_len =

(tail_3, visible_tail_3, base_width_curr);

( !reverse_strand ) {

(

== anchor) {

max_label_w =

(max_label_w, label_w);

(max_label_width_px > 0.0) {

(label_width_px > max_label_width_px) {

label_width_px = max_label_width_px;

((string::npos !=

.find(

)) && (

.length() <= 5))

(reverse_strand) {

xM = inrc.

() - t_w;

inrc.

(), yM - label_h - 1.0), 0);

xM + t_w, yM - label_h - 1.0), 0);

(anchor_range.

()) {

<<

);

(anchor_range.

()) {

override_color =

;

(aln_r_s > aln_r_e) {

(aln_r_s, aln_r_e);

(

== anchor) {

reverse_strand =

(

->IsAverageable()) {

override_color, read_status_color);

override_color, read_status_color);

gl.

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

start /= base_width_anchor;

start /= base_width_anchor;

(

<<

strandLabel[2] = {

,

};

strandLabel[0] = reverse_strand ?

:

;

strandLabel[0] = reverse_strand ?

:

;

strandLabel[0] = reverse_strand ?

:

;

strandLabel[0] = reverse_strand ?

:

;

(label_w > max_label_width_px) {

label_w = max_label_width_px;

xM + label_w, y - gl.

(&l_font) - 1.0), 0);

(anchor_range.

()) {

(aln_r_s > aln_r_e) {

(aln_r_s, aln_r_e);

(aln_range.

() > 2) {

unique_ptr<IAlnSegmentIterator> p_it(

ab = mhndl.

();

rb = hndl.

();

frame_shift_f = start % base_width_curr;

frame_shift_t = 2 - stop % base_width_curr;

(base_width_anchor == 3) {

frame_shift_f = sStart % base_width_anchor;

frame_shift_t = 2 - sStop % base_width_anchor;

(sStart > sStop) {

(sStart, sStop);

(frame_shift_f, frame_shift_t);

stop /= base_width_curr;

start /= base_width_curr;

sStart /= base_width_anchor;

sStop /= base_width_anchor;

sStop += frame_shift_t;

sStart -= frame_shift_f;

stop += frame_shift_t;

start -= frame_shift_f;

seq, mseq, tmp_seq, visible_seq;

s_vec.

(start, stop + 1, tmp_seq);

ms_vec.

(sStart, sStop + 1, mseq);

visible_seq = tmp_seq;

(reverse_strand) {

(seq, tmp_seq);

translated_seq;

seq_candidate = mseq;

(reverse_strand) {

(reverse_strand) {

translated_seq = tmp_seq;

.SetFrom(

.GetFrom() - frame_shift_f);

.SetTo(

.GetTo() + frame_shift_t);

start_base = frame_shift_f % base_width_anchor;

stop_base =

(stop - start + 1 - frame_shift_t % base_width_anchor,

(

bp = start_base; bp < stop_base; bp++) {

pos = sStart + bp + addon;

= bp < seq.size() && bp < mseq.size()

&& seq[bp] == mseq[bp];

pos = sStart + bp * 3 + addon + 1;

= bp < seq.size() && bp < translated_seq.size()

&& seq[bp] == translated_seq[bp];

bp_pos = bp / 3;

= bp_pos < seq.size() && bp_pos < translated_seq.size()

&& mseq[bp_pos] == translated_seq[bp_pos];

(pos < (seg_start - 0.5))

(pos > (seg_stop + 1))

unique_ptr<IAlnScoreIterator> score_iter(

->GetScoreIterator(

));

score_iter->MoveTo(bp);

bases[0] = visible_seq[bp];

pos, center_y + fs * 0.5,

);

:

;

:

;

* char_msg =

;

(width > long_msg_width) {

msg_width = long_msg_width;

(width > short_msg_width) {

msg_width = short_msg_width;

(width > char_msg_width) {

msg_width = char_msg_width;

msg_spacing = char_msg_width * 4.0;

(width < msg_width + msg_spacing*2.0) {

vector<TModelPoint> pts;

bottom_y =

;

(pos <

() + seq_w - seq_char_width) {

pts.push_back(

(pos, center_y + fs * 0.5));

pts.push_back(

(pos, center_y - fs * 0.5));

bottom_y = !bottom_y;

pos += seq_char_width;

(pos >

() - (seq_w - seq_char_width)) {

pts.push_back(

(pos, center_y + fs * 0.5));

pts.push_back(

(pos, center_y - fs * 0.5));

bottom_y = !bottom_y;

pos -= seq_char_width;

fraction,

)

override_color,

TR rasterizer(scoreStart, scoreEnd, fromM, toM);

pix = { 0.0f, 0.0f,

};

unique_ptr<IAlnScoreIterator> score_iter(

->GetScoreIterator(

));

(aln_seg_it && it) {

(it && start1 > stop2) {

stop2 = it.

();

(start1 > stop2) {

from = std::max<int>(start1, start2);

to = std::min<int>(stop1, stop2);

act_from /= base_width_anchor;

act_to /= base_width_anchor;

(act_from > act_to) {

(act_from, act_to);

(act_from <= act_to) {

rasterizer.AddInterval(act_from, act_to + 1.0 / base_width_anchor, pix,

);

TR::TRaster& raster = rasterizer.GetRaster();

eps = 0.0001f;

shift_x = scoreStart;

(

= 0;

< raster.size(); ) {

start =

+ shift_x;

& sc_pix = raster[

];

(++

< raster.size() && raster[

] == sc_pix);

= read_status_color;

off_y = sc_pix.

? GapOffset : 0;

x2 =

+ shift_x;

gl.

(GL_LINES);

gl.

(start, yy + height - off_y);

gl.

(start, yy + off_y, x2, yy + height - off_y);

eps = 0.00001f;

override_color,

(seq_range.

())

TR rasterizer(scoreStart, scoreEnd, fromM, toM);

unique_ptr<IAlnScoreIterator> score_it(

->GetScoreIterator(

));

(aln_seg_it && it) {

(it && start1 > stop2) {

stop2 = it.

();

(start1 > stop2) {

from = std::max<int>(start1, start2);

to = std::min<int>(stop1, stop2);

pix = { 0.0f, 0.0f, 0.0f, 0.0f, 0.0f,

};

act_from /= base_width_anchor;

act_to /= base_width_anchor;

(act_from > act_to) {

(act_from, act_to);

(act_from <= act_to && act_from <=toM) {

rasterizer.AddInterval(act_from, act_to + 1.0 / base_width_anchor, pix,

);

= (act_to - act_from) + 1;

rasterizer.AddInterval(act_from, act_to + 1.0 / base_width_anchor, pix,

);

TR::TRaster& raster = rasterizer.GetRaster();

shift_x = scoreStart;

eps = 0.001f;

value_scale = value_limits.

() - value_limits.

();

(value_scale <= 0)

(

= 0;

< raster.size(); ) {

start =

+ shift_x;

& sc_pix = raster[

];

(++

< raster.size() && raster[

] == sc_pix);

= override_color ?

sc =

(1.0f, ((sc - value_limits.

()) / value_scale));

alpha = 1.0f - sc * 0.75f;

alpha =

(1.0f, 0.25f + sc_pix.

* 0.75f);

x2 =

+ shift_x;

gl.

(GL_LINES);

gl.

(start, yy, x2, yy + height);

gl.

(GL_LINES);

<<

);

intervals.push_back(

);

(aln_r_s > aln_r_e) {

(aln_r_s, aln_r_e);

= target_row;

=

(0, 1 - anchor);

(aln_r.

())

start /= base_width_anchor;

stop /= base_width_anchor;

(!intervals.empty()) {

intervals.back().SetTo(stop);

intervals.push_back(

(start, stop) );

shown =

;

(

.reverse_strand) {

start *=

.base_width_anchor;

start += aln_stop + 1;

end *=

.base_width_anchor;

end += aln_stop + 1;

start *=

.base_width_anchor;

start = aln_start - start;

end *=

.base_width_anchor;

end = aln_start - end;

start *=

.base_width_anchor;

end *=

.base_width_anchor;

start *=

.base_width_anchor;

end *=

.base_width_anchor;

tail_len_pix += label_space_pix;

(tail_label_len > 0) {

tail_len = visible_tail*base_width_curr;

(visible_tail < tail) {

(tail_label_len > 0) {

override_color =

;

((*iter)->GetType().IsStr() &&

(*iter)->GetType().GetStr() ==

) {

override_color =

;

((*iter)->GetType().IsStr() &&

(*iter)->GetType().GetStr() ==

) {

override_color =

;

User-defined methods of the data storage class.

User-defined methods of the data storage class.

User-defined methods of the data storage class.

double CompressLength(double len)

static void FSetPixMaxCoverage(SScPix &dst, const SScPix &src, float fraction, bool)

a pixel with the Max coverage (fraction) overrides all attributes

static const int kCompactLabelSpace_h

static const TSeqPos kTailGlyphLen

static float kMinSegDistance

static const int kLabelSpace_v

static const int kAlignRowSpace

static void FSetPix2(SScPix2 &dst, const SScPix2 &src, float fraction, bool long_seg)

accumulate weighted scores

static const TSeqPos kCompactTailGlyphLen

static const int kLabelSpace_h

static const TModelUnit kPWAlignPackLevel

ELabelPosition m_LabelPos

@ eNormal

no compact mode

@ eExtremeCompact

extreme compact mode

CGlTextureFont m_LabelFont

ECompactMode m_CompactMode

Alignment layout compact mode.

CRgbaColor m_UnalignedSequence

bool m_ShowIdenticalBases

bool m_ShowUnalignedTailsForTrans2GenomicAln

CRgbaColor m_NonConsensus

EUnalignedTailsMode m_UnalignedTailsMode

@ ePos_Above

above the rendered bar

@ ePos_Side

always on 5' side

CGlAttrGuard - guard class for restoring OpenGL attributes.

@ fNoCaching

The tooltip for this feature should not be cached.

int m_Flags

area flags, will need to replace m_Type

bool m_PositiveStrand

the default is true

static string GetAlignSignature(const objects::CSeq_align &align, const objects::CSeq_loc &on_loc, objects::CScope *scope, const objects::CSeq_annot_Handle &annot_handle)

bool IsHorizontal() const

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

void DrawTriangle(TModelUnit x1, TModelUnit y1, TModelUnit x2, TModelUnit y2, TModelUnit x3, TModelUnit y3, bool border=false) const

CGlPane * GetGlPane()

inline method implementations

TModelRange IntersectVisible(const CSeqGlyph *obj) const

TVPUnit SeqToScreenX(const TModelUnit &size) const

void DrawLineStrip(const vector< TModelPoint > &points) const

void DrawUnalignedTail(TModelUnit x1, TModelUnit x2, TModelUnit y1, TModelUnit y2, bool is_polya, const CRgbaColor &color) const

void DrawLine(TModelUnit x1, TModelUnit y1, TModelUnit x2, TModelUnit y2) const

void DrawStippledLine(TModelUnit x1, TModelUnit y1, TModelUnit x2, TModelUnit y2, int factor=2, unsigned short pattern=0xAAAA) const

objects::CScope & GetScope()

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

const TModelUnit & GetScale() const

void DrawSelection(const TModelRect &rc) const

TModelUnit SeqToScreen(const TModelUnit &size) const

convert from sequence positions to screen pixels

TModelUnit SeqToScreenXInModelUnit(const TModelUnit &size) const

TModelUnit ScreenToSeq(const TModelUnit &size) const

convert from screen pixels to sequence positions

bool IsOverviewMode() const

bool IsFlippedStrand() const

bool WillSeqLetterFit() const

is it enougth space to sequence letters.

void DrawDisk2(const TModelPoint &p, TModelUnit size, CRgbaColor color)

const CRgbaColor & GetSelLabelColor() const

void DrawLine_NoAA(TModelUnit x1, TModelUnit y1, TModelUnit x2, TModelUnit y2) const

TSeqPos GetViewWidth() 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

void DrawGreaterLessSign(TModelUnit x1, TModelUnit x2, TModelUnit bar_h, bool negative) const

class CRgbaColor provides a simple abstraction for managing colors.

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)

virtual TModelUnit GetRight() const

virtual void SetWidth(TModelUnit w)

virtual void SetLeft(TModelUnit l)

virtual TModelUnit GetTop() const

virtual TModelUnit GetHeight() const

virtual bool LessBySeqPos(const CSeqGlyph &obj) const

compare this object to another based on glyph sequence position.

float GetFadeFactor() const

size_t GetTearline() const

size_t GetVisible() const

virtual TModelUnit GetWidth() const

virtual TModelUnit GetLeft() const

TModelRect GetModelRect() const

get the bounding box.

vector< CHTMLActiveArea > TAreaVector

virtual TModelUnit GetBottom() const

static SIZE_TYPE Reverse(const string &src, TCoding src_coding, TSeqPos pos, TSeqPos length, string &dst)

static SIZE_TYPE ReverseComplement(const string &src, TCoding src_coding, TSeqPos pos, TSeqPos length, string &dst)

static SIZE_TYPE Complement(const string &src, TCoding src_coding, TSeqPos pos, TSeqPos length, string &dst)

ENa_strand GetSeqStrand(TDim row) const

Get strand (the first one if segments have different strands).

@ eRight

Towards higher aln coord (always to the right)

@ eLeft

Towards lower aln coord (always to the left)

@ eBackwards

Towards lower seq coord (to the left if plus strand, right if minus)

@ eForward

Towards higher seq coord (to the right if plus strand, left if minus)

virtual EPolyATail HasPolyATail() const =0

Check if there is any unaligned polyA tail.

pair< ECigarOp, size_t > TCigarPair

virtual void GetUnalignedTails(TSignedSeqPos &start_tail, TSignedSeqPos &end_tail, bool clipped=true) const

virtual const TCigarPair * GetCigarAtAlnPos(int row, TSignedSeqPos pos) const

virtual bool IsRegular() const

virtual bool IsNegativeStrand(TNumrow row) const =0

int GetPartialFlags() const

virtual const objects::CBioseq_Handle & GetBioseqHandle(IAlnExplorer::TNumrow row) const =0

virtual TSeqRange GetAlnRangeWithTails() const

IAlnExplorer::TNumrow TNumrow

virtual TSeqPos GetSeqStart(TNumrow row) const =0

virtual const objects::CSeq_id & GetSeqId(TNumrow row) const =0

int GetGenCode(IAlnExplorer::TNumrow row) const

virtual TSignedRange GetSeqAlnRange(TNumrow row) const =0

virtual IAlnExplorer::TNumrow GetQuery() const

virtual TSeqPos GetSeqStop(TNumrow row) const =0

virtual TSignedSeqPos GetAlnPosFromSeqPos(TNumrow row, TSeqPos seq_pos, IAlnExplorer::ESearchDirection dir=IAlnExplorer::eNone, bool try_reverse_dir=true) const =0

virtual TSeqPos GetFrom() const =0

virtual float GetAttr() const =0

virtual TSeqPos GetTo() const =0

Alignment segment iterator interface.

@ eAllSegments

Iterate all segments.

@ eSkipGaps

Skip gap segments (show only aligned ranges)

Alignment segment interface.

virtual const TSignedRange & GetRange(void) const =0

Get the selected row range.

@ fAligned

Aligned segment.

@ fIndel

Either anchor or the selected row is not present in the segment.

@ fUnaligned

The range on the selected sequence does not participate in the alignment (the alignment range of the ...

virtual TSegTypeFlags GetType(void) const =0

Get current segment type.

bool IsAligned(void) const

bool IsGap(void) const

Check if there's a gap on the selected row.

virtual const TSignedRange & GetAlnRange(void) const =0

Get alignment range for the segment.

vector< TSeqRange > TIntervals

virtual TSeqPos GetBaseWidth(IAlnExplorer::TNumrow) const =0

virtual string & GetAlnSeqString(IAlnExplorer::TNumrow row, string &buffer, const IAlnExplorer::TSignedRange &aln_range) const =0

virtual IAlnExplorer::TNumrow GetNumRows() const =0

virtual IAlnExplorer::TNumrow GetAnchor() const =0

virtual IAlnSegmentIterator * CreateSegmentIterator(IAlnExplorer::TNumrow, const IAlnExplorer::TSignedRange &, IAlnSegmentIterator::EFlags) const =0

virtual TSignedSeqPos GetSeqPosFromAlnPos(IAlnExplorer::TNumrow for_row, TSeqPos aln_pos, IAlnExplorer::ESearchDirection dir=IAlnExplorer::eNone, bool try_reverse_dir=true) const =0

bool IsConsensusSplice(const string &splice5, const string &splice3)

Consensus splice is GY..AG or AT..AC.

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

unsigned int TSeqPos

Type for sequence locations and lengths.

#define ITERATE(Type, Var, Cont)

ITERATE macro to sequence through container elements.

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)

#define LOG_POST(message)

This macro is deprecated and it's strongly recomended to move in all projects (except tests) to macro...

void Error(CExceptionArgs_Base &args)

const string & GetMsg(void) const

Get message string.

void Warning(CExceptionArgs_Base &args)

bool IsSimplified() const

void x_DrawInserts(const SDrawContext &ctx) 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.

void x_CalcIntervals(TIntervals &intervals, int target_row=-1) const

void x_DrawStrandIndicators(const SDrawContext &ctx) const

virtual void GetHTMLActiveAreas(TAreaVector *p_areas) const

Get html active areas.

virtual bool HasObject(CConstRef< CObject > obj) const

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

virtual bool LessBySeqPos(const CSeqGlyph &obj) const

compare this object to another based on glyph sequence position.

vector< TModelRange > TMUnitRanges

void x_RenderAveragableScores(TModelUnit yy, TSignedSeqRange aln_range, TSeqRange seq_range, TModelUnit height, int row, bool override_color, const CRgbaColor &read_status_color) const

void x_DrawMultiAlignLabel(int row, TModelUnit y) const

void x_DrawUnalignedBar(const ETail tail, const SDrawContext &ctx, const CRgbaColor &c_fg) const

CAlignGlyph(CConstRef< IAlnGraphicDataSource > aln_mgr, const objects::CSeq_align_Handle &orig_align, const objects::CSeq_align &mapped_align, int orig_anchor)

virtual CConstRef< CObject > GetObject(TSeqPos pos) const

access our core component - we wrap an object(s) of some sort.

TSeqRange x_ConvertAlnTaillRngToSeqRng(const ETail tail, const SDrawContext &ctx, const TSeqRange &aln_range) const

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

retrieve CObjects corresponding to this CSeqGlyph.

void x_DrawMultiAlign() const

void x_GetOverrideColor(bool &override_color, CRgbaColor &read_status_color) const

TModelUnit x_GetTailLabelWidth(const TSignedSeqPos tail) const

TIntervals m_Intervals

intervals.

virtual string GetSignature() const

return signature for this glyph.

void GetTitle(string *title, CLabel::ELabelType type) const

void x_DrawNonConsensusSpliceSites(const SDrawContext &ctx) const

void x_RenderNonAveragableScores(TModelUnit yy, TSignedSeqRange aln_range, TSeqRange seq_range, TModelUnit height, int row, bool override_color, const CRgbaColor &read_status_color) const

void x_DrawNoScoreAlign(const SDrawContext &ctx, const CRgbaColor &c_fg) const

void DrawPWAlignElem(const TModelRect &rcm, bool selected, bool show_label, const CRgbaColor &c_fg, const CRgbaColor &c_seq, const CRgbaColor &c_mis) const

virtual TSeqRange GetRange(void) const

get the total range of this object.

const IAlnGraphicDataSource & GetAlignMgr(void) const

Inline methods.

void x_DrawIntronsAndInternalUnalignedRegions(const SDrawContext &ctx, TSignedSeqPos from, TSignedSeqPos to) const

void x_DrawGaps(const SDrawContext &ctx) const

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

Get the tooltip if available.

CConstRef< CAlignmentConfig > m_Config

const objects::CSeq_align_Handle & GetOrigAlignment(void) const

virtual bool IsClickable() const

Query if this glyph is clickable.

void x_DrawUnalignedRowSequence(const ETail tail, const SDrawContext &ctx, const CRgbaColor &c_fg) const

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

access the position of this object.

void x_DrawInternalUnalignedRegions(const SDrawContext &ctx, TMUnitRanges &unaligned_regions) const

CRef< objects::CSeq_loc > m_Location

static bool IsVDBAccession(const string &acc)

Check if string starts with ("SRA", "SRR", "DRR", "ERR")

TModelUnit GetBarHeight() const

TModelUnit x_GetTailWidth(const TSignedSeqPos tail, const TSignedSeqPos visible_tail, const TSignedSeqPos base_width_curr) const

virtual const TIntervals & GetIntervals(void) const

access sub-intervals (if any).

void x_DrawAlignRowSequence(TModelUnit center_y, int row, const CRgbaColor &c_fg, const CRgbaColor &c_seq, const CRgbaColor &c_mis) const

TSeqRange x_GetAlnTailRange(const ETail tail, const SDrawContext &ctx) const

void x_DrawSimplified(const SDrawContext &ctx, const CRgbaColor &c_fg) const

virtual void x_UpdateBoundingBox()

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

CConstRef< IAlnGraphicDataSource > m_AlnMgr

pointer to the actual alignment information.

bool x_ShowUnalignedTails(TModelUnit align_len) const

bool m_DisableTooltipsCaching

Indicates whether the front-end can cache the tooltips.

void x_DrawTailSequences(const SDrawContext &ctx, const CRgbaColor &c_fg) const

void x_DrawPWAlign() const

const objects::CSeq_align & GetAlignment(void) const

CConstRef< objects::CSeq_align > m_SeqAlign

CConstIRef< ISGAlnScore > m_Score

objects::CSeq_align_Handle m_OrigSeqAlign

int m_OrigAnchor

The anchor row number in original Seq-algin, not alnmgr.

void x_DrawTailGlyphs(const SDrawContext &ctx, bool show_label, const CRgbaColor &c_fg) const

virtual void Scalef(GLfloat x, GLfloat y, GLfloat z)=0

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 Color3f(GLfloat r, GLfloat g, GLfloat b)

IRender & GetGl()

convenience function for getting current render manager

void Vertex2d(GLdouble x, GLdouble y)

TVPRect & GetViewport(void)

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

virtual TModelUnit TextWidth(const CGlTextureFont *font, const char *text) const =0

void Color4d(GLdouble r, GLdouble g, GLdouble b, GLdouble a)

virtual void PopMatrix()=0

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.

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

TModelRect & GetVisibleRect(void)

CGlRect< TModelUnit > TModelRect

virtual void Disable(GLenum glstate)=0

glDisable()

virtual void LineWidth(GLfloat w)=0

Set line width for drawing: glLineWidth()

TModelUnit GetScaleY(void) const

CGlPoint< TModelUnit > TModelPoint

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 PushMatrix()=0

string Truncate(const char *text, TModelUnit w, ETruncate trunc=eTruncate_Ellipsis) const

Truncate text to the secified width.

void SetDataSource(const CConstRef< IAlnGraphicDataSource > &data_source)

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

void SetAnchorRow(int anchor)

void SetFlippedStrands(bool flipped=true)

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

add a row with a cell, spanning across all columns

void Set(float r, float g, float b)

set the color from an Fl_Color

float GetBlue(void) const

float GetGreen(void) const

void SetScale(double scale)

void Lighten(float scale)

static CRgbaColor Interpolate(const CRgbaColor &color1, const CRgbaColor &color2, float alpha)

Interpolate two colors.

static bool IsPolyA(const objects::CBioseq_Handle &bsh, TSeqPos start, TSeqPos stop)

float GetRed(void) const

Get specific channels in floating point values.

const string AsFastaString(void) const

CConstRef< CSeq_id > GetSeqId(void) const

virtual void Assign(const CSerialObject &source, ESerialRecursionMode how=eRecursive)

Override Assign() to incorporate cache invalidation.

void SetId(CSeq_id &id)

set the 'id' field in all parts of this location

const CSeq_id & GetId(const CSeq_loc &loc, CScope *scope)

If all CSeq_ids embedded in CSeq_loc refer to the same CBioseq, returns the first CSeq_id found,...

TSeqPos GetLength(const CSeq_id &id, CScope *scope)

Get sequence length if scope not null, else return max possible TSeqPos.

static void Translate(const string &seq, string &prot, const CGenetic_code *code, bool include_stop=true, bool remove_trailing_X=false, bool *alt_start=NULL, bool is_5prime_complete=true, bool is_3prime_complete=true)

Translate a string using a specified genetic code.

@ fIs5PrimePartial

= 0x4 Translate first codon even if not start codon (because sequence is 5' partial)

TSeqPos GetBioseqLength(void) const

CSeqVector GetSeqVector(EVectorCoding coding, ENa_strand strand=eNa_strand_plus) const

Get sequence: Iupacna or Iupacaa if use_iupac_coding is true.

@ eCoding_Iupac

Set coding to printable coding (Iupacna or Iupacaa)

void GetSeqData(TSeqPos start, TSeqPos stop, string &buffer) const

Fill the buffer string with the sequence data for the interval [start, stop).

TObjectType * GetPointer(void) const THROWS_NONE

Get pointer,.

TObjectType * GetPointer(void) THROWS_NONE

Get pointer,.

void Reset(void)

Reset reference object.

position_type GetLength(void) const

TThisType IntersectionWith(const TThisType &r) const

position_type GetToOpen(void) const

TThisType & Set(position_type from, position_type to)

CRange< TSeqPos > TSeqRange

typedefs for sequence ranges

CRange< TSignedSeqPos > TSignedSeqRange

#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.

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

Convert UInt to string.

@ fWithCommas

Use commas as thousands separator.

static const char label[]

void SetFrom(TFrom value)

Assign a value to From data member.

TTo GetTo(void) const

Get the To member data.

TFrom GetFrom(void) const

Get the From member data.

void SetTo(TTo value)

Assign a value to To data member.

const TDonor_after_exon & GetDonor_after_exon(void) const

Get the Donor_after_exon member data.

TGenomic_start GetGenomic_start(void) const

Get the Genomic_start member data.

const TAcceptor_before_exon & GetAcceptor_before_exon(void) const

Get the Acceptor_before_exon member data.

bool IsSetAcceptor_before_exon(void) const

splice sites Check if a value has been assigned to Acceptor_before_exon data member.

list< CRef< CUser_object > > TExt

list< CRef< CSpliced_exon > > TExons

const TExons & GetExons(void) const

Get the Exons member data.

const TBases & GetBases(void) const

Get the Bases member data.

TGenomic_end GetGenomic_end(void) const

Get the Genomic_end member data.

bool IsSetDonor_after_exon(void) const

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

unsigned int

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

constexpr auto sort(_Init &&init)

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

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

static int match(PCRE2_SPTR start_eptr, PCRE2_SPTR start_ecode, uint16_t top_bracket, PCRE2_SIZE frame_size, pcre2_match_data *match_data, match_block *mb)

static SLJIT_INLINE sljit_ins msg(sljit_gpr r, sljit_s32 d, sljit_gpr x, sljit_gpr b)

#define row(bind, expected)

represents a pixel with two scores, one corresponds to a gap interval, another - to an aligned segmen...

bool operator==(const SScPix2 &other) const

represents a pixel with a score, if several intervals cover a pixel, the interval with the maximum co...

float m_MaxCoverage

score assigned to the pixel

bool m_Gap

fraction of the pixel corresponding to the m_Score

bool operator==(const SScPix &other) const

true if this is a gap interval

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