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

(

.GetFrom() <

.GetFrom()) {

(

.GetFrom() >

.GetFrom()) {

(

.GetTo() <

.GetTo()) {

, m_Location(&

.GetLocation())

, m_HideLabel(

)

, m_ProjectedFeat(

)

, m_RulerType(eNoRuler)

, m_LinkedFeat(LinkedFeatDisplay)

, m_HideLabel(

)

, m_ProjectedFeat(

)

, m_RulerType(eNoRuler)

, m_LinkedFeat(LinkedFeatDisplay)

(comp(*

, *feat));

CreateObjectInterface<IGuiObjectInfo>(scoped_obj,

));

( !gui_info )

;

(loc->

()) {

((

)at_p != -1) {

aligned = aln_mgr->GetQuery();

(aln_mgr->GetBaseWidth(anchor) == 3) {

pos *= aln_mgr->GetBaseWidth(anchor);

fract_part = (p.

() - floor(p.

())) * 100.;

off =

(2, fract_part / 33);

at_p = aln_mgr->GetSeqPosFromSeqPos(aligned, anchor, pos);

(aln_mgr->IsNegativeStrand(aligned))

at_p = aln_mgr->GetSeqPosFromSeqPos(aligned, anchor, pos);

& prod_range = mi.m_MappedProdRange;

mapping_info.emplace_back(prod_int, mi.m_MappedInt);

(

&&

->GetSeqDS()) {

isTooltipGeneratedBySvc(

);

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

(!isTooltipGeneratedBySvc) {

gui_info->GetLinks(tt,

);

().GetInt().GetFuzz_from().IsRange()) {

sColorTheme(

);

sColorKey(

);

sColorKey =

;

sColorKey =

;

sColorKey =

;

sColorKey =

;

(sColorKey !=

) {

(idx > 0 && idx <

.size()) {

is_db_xref =

().IsSetDbxref();

(

.NotEmpty()) {

(

.NotEmpty()) {

(

.NotEmpty()) {

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

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

&&

(*iter)->GetFieldRef(

) &&

(*iter)->GetFieldRef(

)->GetData().GetBool() &&

((*iter)->GetFieldRef(

) &&

(*iter)->GetFieldRef(

)->GetData().GetBool()) {

tooltip->SetTrustedData(

);

s = tooltip->Render();

p_areas->push_back(area);

<<

sAdditionalInfo.clear();

((*iter)->IsSetSeq() && (*iter)->GetSeq().IsLiteral()) {

= (*iter)->GetSeq().GetLiteral().GetLength();

}

(var.

()) {

}

(var.

()) {

& var_type = feat.

(

);

( !var_type.empty() ) {

& identity = feat.

(

);

( !identity.empty() ) {

(identity_num > 99.0) {

}

(identity_num > 98.0) {

}

(identity_num > 90.0) {

(

)idx;

isRelatedGlyphSelected;

(pParentLayoutGroup) {

(

iSeqGlyphs=0; iSeqGlyphs < pParentLayoutGroup->

(); ++iSeqGlyphs) {

(pParentLayoutGroup->

(

(iSeqGlyphs))->IsSelected()) {

(pParentLayoutGroup) {

(

iSeqGlyphs=0; iSeqGlyphs < pParentLayoutGroup->

(); ++iSeqGlyphs) {

(pParentLayoutGroup->

(

(iSeqGlyphs))->IsSelected()) {

base += bar_height * 0.5;

x_IntersectVisible<TModelUnit>(

(model_rect.

(), model_rect.

()), left, right);

prod_len = prod_vec.

();

gen_seq.reserve(prod_len);

& prod_int = *iter.first;

& gen_int = *iter.second;

t_from = prod_int.GetFrom();

(t_from > pre_t_to)

gen_seq.append(t_from - pre_t_to,

);

vec.

(gen_int.GetFrom(), gen_int.GetTo() + 1, tmp_seq);

neg = gen_int.IsSetStrand() && gen_int.GetStrand() ==

;

0,

(tmp_seq.length()), seq);

pre_t_to = prod_int.GetTo() + 1;

prod_out[1] =

;

& prod_int = *map_it.first;

& gen_int = *map_it.second;

neg = gen_int.IsSetStrand() && gen_int.GetStrand() ==

;

step = neg ? -1 : 1;

gen_range(gen_int.GetFrom(), gen_int.GetTo());

(current_exon !=

.end() && current_exon->GetFrom() > gen_range.

()) {

(current_exon !=

.end() && current_exon->GetTo() < gen_range.

()) {

prod_range(prod_int.GetFrom(), prod_int.GetTo());

(prod_pos < prod_stop) {

mismatch = (prod_seq[prod_pos] != gen_seq[prod_pos]);

prod_out[0] = prod_seq[prod_pos];

(prev_gen != 0) {

(prev_prod->GetTo() + 1 != prod_int.GetFrom()) {

c_pos = neg ? gen_int.GetTo() + 1 : gen_int.GetFrom();

(c_pos, base - font_height, base + font_height, base);

(prev_gen->GetFrom() - 1 != gen_int.GetTo()) {

c_pos = prev_gen->GetFrom() - 1;

(prev_gen->GetTo() + 1 != gen_int.GetFrom()) {

c_pos = prev_gen->GetTo() + 1;

prev_gen.

(&gen_int);

prev_prod.

(&prod_int);

(visible_range_pos.

() < min_text_w_pos) {

sAdditionalInfo;

(!sAdditionalInfo.empty()) {

all_same_type = -1;

(parent !=

) {

(all_same_type == -1 ) {

all_same_type =

->AllChildrenSameType() ? 1 : 0;

track_title =

->GetFullTitle();

start_idx =

.find_first_not_of(

);

stop_idx =

.find_last_not_of(

);

= stop_idx-start_idx;

(all_same_type == 1 &&

);

sLabelTextOut;

sLabelTypeText;

(visible_range.

() > LabelTypeWidth * 4) {

+= sLabelTextOut;

sLabelTextOut =

;

base += font_height;

->

(&font, sLabelTextOut.c_str(), LabelX, LabelY,

,

);

(exon_int.

())

side_lbl{

};

LabelVisibleWidth = (FeatureBarLeft < visible_range.

() ? 0 : FeatureBarLeft - visible_range.

());

LabelVisibleWidth = (FeatureBarRight > visible_range.

() ? 0 : visible_range.

() - FeatureBarRight);

(FeatureBarLeft < visible_range_pos.

() ? 0 : FeatureBarLeft - visible_range_pos.

())

(FeatureBarRight > visible_range_pos.

() ? 0 : visible_range_pos.

() - FeatureBarRight));

(AvailableLabelVisibleWidthPos < m_Context->GetMinLabelWidthPos(font)) {

(label_width_px > max_width_px) {

label_width_px = max_width_px;

fl_content = font.

(fl_content.c_str(), label_width_px);

((string::npos != fl_content.find(

)) && (fl_content.length() <= 5))

label_base += (font_height * 0.5);

label_clear_base = label_base;

(bar_height > font_height) {

label_clear_height = bar_height;

label_clear_base = floor(base) + (label_clear_height * 0.5);

label_x_pos = visible_range_pos.

();

(label_x_pos >

()) {

(label_x_pos, label_clear_base + 1, label_x_pos + label_width_pos,

label_clear_base - label_clear_height - 1), 0);

label_x_pos = visible_range_pos.

() - label_width_pos;

label_clear_base - label_clear_height - 1), 0);

label_base,

,

);

(FeatureBarLeft < visible_range.

() ? 0 : FeatureBarLeft - visible_range.

())

(FeatureBarRight > visible_range.

() ? 0 : visible_range.

() - FeatureBarRight));

sAdditionalInfo;

(AvailableAdditionalInfoVisibleWidthPos < m_Context->GetMinLabelWidthPos()) {

(info_width_px > max_width_px) {

info_width_px = max_width_px;

sAdditionalInfo = font.

(sAdditionalInfo.c_str(), info_width_px);

info_base += (font_height * 0.5);

info_clear_base = info_base;

(bar_height > font_height) {

info_clear_height = bar_height;

info_clear_base = floor(base) + (info_clear_height * 0.5);

info_x_pos = visible_range.

();

(info_x_pos >

()) {

(info_x_pos, info_clear_base + 1, info_x_pos + info_width_pos,

info_clear_base - info_clear_height - 1), 0);

info_x_pos = visible_range.

() - info_width_pos;

info_clear_base - info_clear_height - 1), 0);

info_base,

,

);

(loc_it || loc_it.

()) {

has_product =

().IsSetProduct();

display_options = 0;

GetCDSFrame = [&]() {

(

.GetData().GetCdregion().IsSetFrame() &&

.GetData().GetCdregion().GetFrame() > 1) {

.GetData().GetCdregion().GetFrame() - 1;

id1->SetBaseWidth(1);

id2->SetBaseWidth(1);

(protein_scale) {

(loc_it || loc_it.

()) {

id1->SetBaseWidth(1);

.SetFirstFrom(seq_length -

.GetFirstToOpen());

.SetReversed( !

.IsReversed() );

aln_reversed->push_back(

);

aln_reversed->Sort();

aln.

(aln_reversed.GetPointer());

vpt.

((

)floor(base_top));

ruler_panel.

(RP);

(

)((x > 0.0) ? floor(x + 0.5) : ceil(x - 0.5));

display_options = 0;

aligned_seq = aln_mgr->GetQuery();

seq_length = aln_mgr->GetSeqLength(aligned_seq);

base_width = aln_mgr->GetBaseWidth(anchor);

id1->SetBaseWidth(1);

id2->SetBaseWidth(1);

(protein_scale) {

glPushAttrib(GL_ALL_ATTRIB_BITS);

anchor_neg = aln_mgr->IsNegativeStrand(anchor);

aligned_neg = aln_mgr->IsNegativeStrand(aligned_seq);

& anchor_range = iter->m_AnchorRange;

& gen_int = *iter->m_MappedInt;

& prod_int = *iter->m_ProductInt;

& prod_range = iter->m_MappedProdRange;

flip = (flip_strand != (anchor_neg || aligned_neg));

prod_interval->SetId().Assign(prod_int.GetId());

prod_interval->SetFrom(prod_range.GetFrom());

prod_interval->SetTo(prod_range.GetTo());

prod_interval->SetStrand(prod_int.GetStrand());

mapped_interval->SetId().Assign(gen_int.GetId());

mapped_interval->SetFrom(gen_from);

mapped_interval->SetTo(gen_to);

mapped_interval->SetStrand(gen_int.GetStrand());

gen_loc->

().Set().push_back(mapped_interval);

->SetFirstFrom(seq_length -

.GetFirstToOpen());

->SetReversed(!

.IsReversed());

seq_from = anchor_range.GetFrom();

seq_to = min<int>(anchor_range.GetTo(), seq_from + (prod_range.GetLength() / base_width) - 1);

(seq_from, seq_to);

rcV.

(gen_from, gen_to + 1);

vpt.

((

)floor(base_top));

ruler_panel.

(RP);

BoundaryYLow = YCenterLine - bar_height * 0.5f;

BoundaryYHigh = YCenterLine + bar_height * 0.5f;

(!display_settings.

()) {

.SetAlpha(0.8f);

x_IntersectVisible<TSeqPos>(SeqRange, from, to);

(SeqRange.

() > pix_size * 2) {

first_pass =

;

vector<TModelRange> labels_range;

has_accessory_label =

;

strand_indicator_color =

.ContrastingColor(

);

strand_indicator_color.

(0.1f);

vector<CConstRef<CSeq_loc>> locs;

(; iter; ++iter) {

return a->GetTotalRange().GetFrom() < b->GetTotalRange().GetFrom();

(

& curr_loc : locs) {

curr = curr_loc->GetTotalRange();

is_visible_region = x_IntersectVisible<TModelUnit>(

(

,

),

,

);

rsiteCutPnt =

;

(curr_loc->IsPnt()) {

rsiteCutPnt =

;

fit = head_size * 1.5 <

(

-

);

adj_to = !neg_strand &&

== SeqRange.

() && fit;

adj_from = neg_strand &&

== SeqRange.

() && fit;

(adj_from || adj_to) {

= to - head_size * 1.5;

= from + head_size * 1.5;

= from + head_size;

fit = tail_size <

(

-

);

adj_to = neg_strand &&

== SeqRange.

() && fit;

adj_from = !neg_strand &&

== SeqRange.

() && fit;

(adj_from || adj_to) {

= from + tail_size * 0.5f;

= to - tail_size * 0.5f;

= from + tail_size;

= from + tail_size;

intron_f = prev_to_x;

intron_f = prev_from_x;

(intron_f > intron_t)

(intron_f, intron_t);

x_IntersectVisible<TModelUnit>(

(intron_f, intron_t), intron_f, intron_t);

(intron_f < intron_t) {

glPushAttrib(GL_LINE_BIT);

gl.

(GL_LINE_STIPPLE);

gl.

(GL_LINE_STIPPLE);

gl.

(GL_LINE_STIPPLE);

gl.

(GL_LINE_STIPPLE);

intron_f + (intron_t - intron_f) * 0.5f;

gl.

(GL_LINE_STIPPLE);

gl.

(GL_LINE_STIPPLE);

BoundaryYHigh, color_lite);

gl.

(GL_LINE_STIPPLE);

intron_t - intron_f, apart, bar_height,

(!rsiteCutPnt && is_visible_region) {

gl.

(color_insert);

((

+

) * 0.5 + 0.5, BoundaryYLow, BoundaryYHigh, YCenterLine);

gl.

(color_delete);

(

== curr.

())

gl.

(GL_LINE_SMOOTH);

(prev_exon_rng.

())

prev_exon_rng = exon_rng;

strand_rng = prev_exon_rng;

prev_exon_rng = exon_rng;

accessory_label;

(!accessory_label.empty()) {

(

.Right() >

.Left()) {

clipped_from =

(

.Left(), clipped_from);

clipped_to =

(

.Right(), clipped_to);

clipped_to =

(

.Left(), clipped_to);

clipped_from =

(

.Right(), clipped_from);

(clipped_to-clipped_from >

(1.5) * label_width) {

has_accessory_label =

;

(first_pass && has_accessory_label) {

= (clipped_to - clipped_from) - 1;

kLabelStep = 600;

(

>= label_step * 2) {

has_accessory_label =

;

= rng.

();

from = max<int>(clipped_from,

);

x = max<int>(from - label_width /

(2), 0);

(x >=

|| x >= (clipped_to - label_width))

->

(&font, accessory_label.c_str(), x, YCenterLine,

,

);

labels_range.emplace_back(x, x + label_width);

(is_visible_region) {

strand_indicator_color, neg_strand,

!

, has_accessory_label, &labels_range);

strand_rng.

(0, 0);

(has_accessory_label) {

->

(&font, accessory_label.c_str(), from, YCenterLine,

,

);

(p_start || p_stop) {

curr.

(), BoundaryYHigh, p_start, p_stop,

);

prev_from_x =

? from_x : from_x - 1;

first_pass =

;

((neg_strand && from == SeqRange.

()) || (!neg_strand && to == SeqRange.

())) {

(neg_strand ? from : to + 1, YCenterLine),

head_height,

, neg_strand,

);

(neg_strand ? from : to + 1, YCenterLine),

head_height,

, neg_strand,

);

(neg_strand ? from : to + 1, YCenterLine),

head_height, neg_strand);

((neg_strand && to == SeqRange.

()) || (!neg_strand && from == SeqRange.

())) {

(neg_strand ? to + 1.0 : from, YCenterLine),

tail_height,

, neg_strand);

(neg_strand ? to + 1 : from, YCenterLine),

tail_height,

, neg_strand);

neg_strand ? to + 1 : from, BoundaryYLow, BoundaryYHigh,

tail_height,

, neg_strand);

draw_partial_start = (from == SeqRange.

());

draw_partial_stop = (to == SeqRange.

());

BoundaryYHigh, draw_partial_start, draw_partial_stop,

);

(p_start || p_stop) {

(neg_strand)

(p_start, p_stop);

BoundaryYHigh, p_start, p_stop,

);

(!prev_exon_rng.

()) {

strand_indicator_color, neg_strand,

!

, has_accessory_label, &labels_range);

->

(SeqPosTriangleMidPointX, BoundaryYLow, SeqPosTriangleMidPointX, BoundaryYHigh);

SeqPosTriangleMidPointX + SeqTriangleHalf, BoundaryYLow - TriangleOffsetY,

SeqPosTriangleMidPointX - SeqTriangleHalf, BoundaryYLow - TriangleOffsetY);

SeqPosTriangleMidPointX + SeqTriangleHalf, BoundaryYHigh + TriangleOffsetY,

SeqPosTriangleMidPointX - SeqTriangleHalf, BoundaryYHigh + TriangleOffsetY);

SeqPosTriangleMidPointX + SeqTriangleHalf, BoundaryYLow - TriangleOffsetY,

SeqPosTriangleMidPointX - SeqTriangleHalf, BoundaryYLow - TriangleOffsetY);

BoundaryYLow = YCenterLine - bar_height * 0.5f;

BoundaryYHigh = YCenterLine + bar_height * 0.5f;

x_IntersectVisible<TSeqPos>(SeqRange, SeqPosFrom, SeqPosTo);

first_pass =

;

SeqRange = iter.GetRange();

SeqPosFrom = SeqRange.

();

SeqPosTo = SeqRange.

();

SeqPosFromIn = SeqPosFrom;

SeqPosToIn = SeqPosTo;

(loc->

()) {

SeqPosFrom = f_SeqRange.

();

SeqPosFromIn = f_SeqRange.

();

SeqPosTo = t_SeqRange.

();

SeqPosToIn = t_SeqRange.

();

( !first_pass ) {

intron_f = SeqPosFrom > prev_to_x ? prev_to_x + 1 : SeqPosTo + 1;

intron_t = SeqPosFrom > prev_to_x ? SeqPosFrom : prev_from_x;

(literal_len >= (

)(SeqPosToIn - SeqPosFromIn)) {

literal_len = SeqPosToIn - SeqPosFromIn - 2;

xm = (SeqPosFromIn + SeqPosToIn) * 0.5;

m = (SeqPosFromIn + SeqPosToIn - literal_len) * 0.5;

= (SeqPosFromIn + SeqPosToIn + literal_len) * 0.5;

(literal_len < half_w * 2.0) {

half_w = literal_len * 0.5;

vector<TModelPoint> points;

points.push_back(

(xm - half_w, YCenterLine));

points.push_back(

(xm - half_w * 0.5, BoundaryYLow - 1.0));

points.push_back(

(xm + half_w * 0.5, BoundaryYHigh + 1.0));

points.push_back(

(xm + half_w, YCenterLine));

gl.

(0.0f, 0.0f, 0.0f);

->

(SeqPosFromIn, BoundaryYLow, SeqPosToIn + 1.0, BoundaryYHigh);

gl.

(color_insert);

((SeqPosFromIn + SeqPosToIn) * 0.5 + 0.5, BoundaryYLow, BoundaryYHigh, YCenterLine);

->

(SeqPosFromIn, BoundaryYLow, SeqPosToIn + 1.0, BoundaryYHigh);

gl.

(color_insert);

(SeqPosToIn + 1.0, BoundaryYLow, BoundaryYHigh, YCenterLine);

}

(UndefinedBreakpointFrom ==

|| UndefinedBreakpointFrom ==

) {

->

(SeqPosFromIn, BoundaryYLow, SeqPosToIn + 1.0, BoundaryYHigh);

(SeqPosFromIn != SeqPosFrom) {

(SeqPosToIn != SeqPosTo) {

(UndefinedBreakpointFrom ==

) {

SeqPosFromIn - tri_width, BoundaryYLow,

);

}

(UndefinedBreakpointFrom ==

) {

->

(SeqPosFromIn - TriangleOffsetX, BoundaryYLow, SeqPosFromIn - TriangleOffsetX, BoundaryYHigh,

SeqPosFromIn - TriangleOffsetX - tri_width, YCenterLine,

);

(UndefinedBreakpointTo ==

) {

->

(SeqPosToIn + 1.0, YCenterLine, SeqPosToIn + 1.0 + tri_width, BoundaryYHigh,

SeqPosToIn + 1.0 + tri_width, BoundaryYLow,

);

}

(UndefinedBreakpointTo ==

) {

->

(SeqPosToIn + TriangleOffsetX + 1.0, BoundaryYLow, SeqPosToIn + TriangleOffsetX + 1.0, BoundaryYHigh,

SeqPosToIn + TriangleOffsetX + 1.0 + tri_width, YCenterLine,

);

first_pass =

;

prev_to_x = SeqPosTo;

prev_from_x = SeqPosFrom;

gl.

(0.0f, 0.0f, 0.0f);

gl.

(1.0f, 1.0f, 1.0f);

->

(x1, YCenterLine - bar_height, SeqPosTo + 1.0, YCenterLine + bar_height);

x1, YCenterLine - bar_height, SeqPosTo + 1.0, YCenterLine + bar_height,

,

);

SeqPosTo, BoundaryYHigh,

,

);

markerHeight = BoundaryYHigh - BoundaryYLow;

( ; iter; ++iter) {

(!curr_loc->

())

->

(pos, BoundaryYHigh, pos + halfMarkerWidth, BoundaryYHigh + markerHeight, pos - halfMarkerWidth, BoundaryYHigh + markerHeight,

);

->

(pos, BoundaryYLow, pos + halfMarkerWidth, BoundaryYLow - markerHeight, pos - halfMarkerWidth, BoundaryYLow - markerHeight,

);

}

(loc.

() &&

}

(loc.

()) {

}

(loc.

() &&

}

(loc.

()) {

shown =

;

(label_width > available_width) {

((string::npos != fl_content.find(

)) && (fl_content.length() <= 5))

feat_id = &feat.

();

feat_id = feat.

().front().GetPointer();

(feat_id->

()) {

sColorFieldNames[]{

,

,

,

};

sUsedColorFieldName;

(

sCheckColorFieldName: sColorFieldNames) {

(display_settings.HasField(sCheckColorFieldName,

,

)) {

sUsedColorFieldName = sCheckColorFieldName;

(sUsedColorFieldName.empty())

ColorAsInt(display_settings.GetField(sUsedColorFieldName,

,

).GetInt8());

c.

((

)((ColorAsInt >> 16) & 0xFF), (

)((ColorAsInt >> 8) & 0xFF), (

)(ColorAsInt & 0xFF));

(

<<

<< err);

&

=

().m_MappedInt->GetId();

(

&& map_it : *

) {

& gen_int = *map_it.m_MappedInt;

& prod_range = map_it.m_MappedProdRange;

& anchor_range = map_it.m_AnchorRange;

num2add = prod_range.GetFrom() - pre_to;

.append(num2add,

);

(prev_anchor > 0 && pre_gen > 0) {

prev_anchor - anchor_range.GetTo() : anchor_range.GetFrom() - prev_anchor;

is_insert = d == 0;

num2add = gen_neg ? pre_gen - gen_int.GetTo() : gen_int.GetFrom() - pre_gen;

.append(num2add,

);

vec.

(gen_int.GetFrom(), gen_int.GetTo() + 1, tmp_seq);

0,

(tmp_seq.length()), seq);

pre_to = prod_range.GetTo() + 1;

pre_gen = gen_neg ? gen_int.GetFrom() - 1 : gen_int.GetTo() + 1;

prev_anchor = neg ? anchor_range.GetFrom() - 1: anchor_range.GetTo() + 1;

User-defined methods of the data storage class.

User-defined methods of the data storage class.

User-defined methods of the data storage class.

@ eExtreme_Positional

numerical value

User-defined methods of the data storage class.

User-defined methods of the data storage class.

User-defined methods of the data storage class.

void ConvertSeqLocsToPairwiseAln(CPairwiseAln &aln, const objects::CSeq_loc &loc_1, const objects::CSeq_loc &loc_2, CAlnUserOptions::EDirection direction=CAlnUserOptions::eBothDirections)

Build pairwise alignment from a pair of seq-locs.

static void redundant(Char *flag)

@ fAllowOverlap

allow segments with different orientation

@ fKeepNormalized

Policies:

CAlignRange Represents an element of pairwise alignment of two sequences.

Default IAlnSeqId implementation based on CSeq_id_Handle.

@ eBothDirections

No filtering: use both direct and reverse sequences.

vector< CRgbaColor > TColorCode

const TColorCode & GetColorCode() const

@ eLowIdentity

feature's default color based on feature type

TSeqPos x_GetProtOffset() const

Returns protein translation offset.

bool GetRelatedGlyphSelected() const

virtual void x_Draw() const

The default renderer for this layout object.

string m_sTopLabelPrefix

Prefix to prepend to labels on top.

virtual bool HitTestHor(TSeqPos x, const CObject *obj)

void x_DrawInsertion(TModelUnit SeqPosTriangleMidPointX, TModelUnit BoundaryYLow, TModelUnit BoundaryYHigh, TModelUnit YCenterLine) const

bool x_CanShowStrand(objects::ENa_strand strand) const

TIntervals m_Intervals

intervals (like for features or alignments).

void x_GetUserColor(const objects::CUser_object &display_settings, CRgbaColor &color) const

CRef< objects::CSeq_loc > x_AdjustFrame(const objects::CSeq_loc &loc, TSeqPos offset) const

Adjusts a location to accommodate for the protein translation offset.

void LayoutChanged()

update the layout for everything encompassing this glyph

EUndefinedBpType x_GetUndefinedBp_to(const objects::CSeq_loc &loc) const

ELinkedFeatDisplay m_LinkedFeat

linkage mode for the track where this glyph is residing

virtual void x_UpdateBoundingBox()

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

void x_DrawAdditionalInfo(TModelUnit base) const

virtual bool HasSideLabel() const

Query if there is label and label is on the side.

void SetRelatedGlyphSelected(bool Selected)

CConstRef< CFeatureParams > m_Config

All the configs needed for rendering a feature.

bool x_isDrawn() const

determines whether the glyph should be drawn or not at all (currently children of unselected parents ...

TModelUnit x_GetBarHeight() const

CProjectedMappingInfo m_ProjectedMappingInfo

string m_sFilter

filter (if any) for the track where this glyph is residing

virtual bool IsClickable() const

Query if this glyph is clickable.

bool GetCustomColor(CRgbaColor &color) const

Get the customized color for a given feature.

virtual bool NeedTooltip(const TModelPoint &, ITooltipFormatter &, string &) const

Check if need to show tooltip.

void GetAdditionalInfo(string &sAdditionalInfo) const

Some features may have additional info on the right (alleles for SNPs)

virtual string GetSignature() const

return signature for this glyph.

void x_DrawRSites(const CRgbaColor &color, TModelUnit BoundaryYLow, TModelUnit BoundaryYHigh) const

EUndefinedBpType x_GetUndefinedBp_from(const objects::CSeq_loc &loc) const

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

Get the tooltip if available.

objects::CMappedFeat m_Feature

we store a mapped feature object which in turn holds the original feature.

void x_DrawDeletion(TModelUnit SeqPosTriangleMidPointX, TModelUnit BoundaryYLow, TModelUnit BoundaryYHigh) const

void x_DrawRuler(TModelUnit base, bool protein_scale=false) const

const TMappingInfo & GetMappingInfo() const

virtual bool HasObject(CConstRef< CObject > obj) const

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

bool m_ProjectedFeat

Projected features.

void x_DrawFeatureBar(TModelUnit &base) const

bool m_HideLabel

Force to hide the label.

virtual void SetHideLabel(bool b)

Force to hide label.

virtual bool LessBySeqPos(const CSeqGlyph &obj) const

compare this object to another based on glyph sequence position.

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

retrieve CObjects corresponding to this CSeqGlyph.

virtual CConstRef< CObject > GetObject(TSeqPos pos) const

Retrieve the feature as an object.

bool x_RedundantLabelCheck(const string &label) const

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

access the position of this object.

CFeatGlyph(const objects::CMappedFeat &feat, ELinkedFeatDisplay LinkedFeat=ELinkedFeatDisplay::eLFD_Default)

void x_DrawInnerLabels(TModelUnit base, vector< TModelRange > *labels_range=nullptr, TSeqRange *interval=nullptr) const

void x_DrawProjectedRuler(TModelUnit base, bool protein_scale=false) const

CConstRef< objects::CSeq_loc > m_Location

Mapped location in top sequence coordinate.

bool x_LabelOnLeft() const

true if a label should be placed to the left of the feature bar (provided that it is ePos_Side)

TMappingInfo m_MappingInfo

Feature product sequence mapping info.

bool x_IsProjected() const

void x_DrawLabelWithYPinned(TModelUnit base) const

static bool IsDbVar(const objects::CSeq_feat &feat)

Utility to check if a feature is a structural variation.

void x_MaybeDrawLabelOthers(TModelUnit base) const

bool m_RSite

Flag indicating if this is a restriction site.

virtual bool IsConsensus() const

Check if (intron) feature is consensus or not.

TModelUnit GetBarCenter() const

void x_DrawLabelWithXPinned(TModelUnit &base) const

virtual bool SetSelected(bool f)

Select or deselect this glyph.

void x_DrawRNAProductSequence(TModelUnit base) const

bool x_isExpandable(size_t &nChildren) const

returns true if this glyph is expandable i.e.

void x_MaybeDrawLabelAbove(TModelUnit &base) const

bool x_isCollapsible() const

returns true if this glyph is collapsible i.e.

virtual void GetAccessoryLabel(string &accessory_label) const

Some features may have an accessory label on top (e.g. introns)

const objects::CMappedFeat & GetMappedFeature(void) const

Access a new, fully remapped feature.

string x_GetFeatureId() const

virtual TSeqRange GetRange(void) const

get the total range of this object.

map< CLabel::ELabelType, string > m_Labels

virtual string GetPName() const

persistent name of the glyph should not depend on the instance of the glyph, but should uniquely refl...

void x_DrawFeatureBar_sv(TModelUnit base) const

virtual const TIntervals & GetIntervals(void) const

access sub-intervals (if any).

const objects::CSeq_feat & GetFeature(void) const

Access the original feature.

static size_t GetCustomColorIdx(const objects::CSeq_feat &feat)

Get the customized color idx for a given feature.

virtual void GetHTMLActiveAreas(TAreaVector *p_areas) const

Get html active areas.

void GetLabel(string &label, CLabel::ELabelType type) const

retrieve feature label for a given type

EConnection m_Connections

TModelUnit m_LineWidth

absolute value (in pixel)

TModelUnit m_HeadHeight

ratio to bar height

TModelUnit m_TailHeight

ratio to bar height

CRgbaColor m_NonConsensus

CRef< CCustomFeatureColor > m_CustomColors

custom color code for features with a special attribute.

TModelUnit m_OverviewFactor

ratio to bar height

CGlTextureFont m_LabelFont

TModelUnit GetBarHeight(bool overview) const

ELabelPosition m_LabelPos

@ eBox_Insertion

additional decoration for the box

@ eBox_Deletion

add an inverted triangle to mark a deletion

@ eBox_Line

No box - just a line.

TModelUnit m_BarHeight

absolute size (in pixel)

@ ePos_Side

always on 5' side

@ ePos_Inside

inside the rendered bar

@ ePos_Above

above the rendered bar

bool m_ShowStrandIndicator

static CGuiRegistry & GetInstance()

access the application-wide singleton

string m_Descr

description that can be used as label or tooltip

@ fNoCaching

The tooltip for this feature should not be cached.

@ fIgnorable

feature can be ignored (isca browser feature editing only)

@ fEditable

can be modified (isca browser feature editing only)

string m_ID

area identifier

int m_Flags

area flags, will need to replace m_Type

bool m_PositiveStrand

the default is true

CLayoutGroup is a container of CSeqGlyphs (layout objects).

static void PropagateRelatedSelection(bool isSelected, CSeqGlyph *pGlyph, CSeqGlyph *pGlyphFrom=NULL)

set "RelatedGlyphSelected" in CLayoutGroup-based glyph hierarchies everywhere in the hierarchy contai...

CConstRef< CSeqGlyph > GetChild(int idx) const

Get the layout object at index 'idx'.

size_t GetChildrenNum() const

Get total number of children.

bool IsMaster(const CSeqGlyph *glyph) const

static string GetFeatSignature(const objects::CSeq_feat &feat, objects::CScope *scope, const string &data_source="", const string &sAdditionalInfo="")

A pairwise aln is a collection of ranges for a pair of rows.

void GetAnchorSequence(objects::CScope &scope, string &buffer) const

CConstRef< IAlnGraphicDataSource > m_AlnMgr

const IAlnGraphicDataSource * GetAlignmentDataSource() const

class CRegistryReadView provides a nested hierarchical view at a particular key.

CRenderingContext offers the basic context and utility methods for rendering layout objects in featur...

bool GetIsDrawn(const string &sPName) const

void DrawDisk(const TModelPoint &p, TModelUnit radius, GLint from=0, GLint to=360) const

bool IsHorizontal() const

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

static const int kLabelSpacePx

extra space for side labeling, in screen pixels

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

void Draw3DFletch(TModelUnit pos_x, TModelUnit line_y1, TModelUnit line_y2, TModelUnit tail_height, const CRgbaColor &color, bool neg_strand) const

void DrawPseudoBar(TModelUnit x1, TModelUnit y1, TModelUnit x2, TModelUnit y2, const CRgbaColor &light_color, const CRgbaColor &dark_color) const

CRef< CSGSequenceDS > GetSeqDS() const

const TSeqRange & GetVisSeqRange() const

CGlPane * GetGlPane()

inline method implementations

const TModelUnit & GetOffset() const

TModelRange IntersectVisible(const CSeqGlyph *obj) const

TModelUnit GetMinLabelWidthPos() const

TSeqPos GetVisSeqTo() const

void Draw3DQuad_HorzLines(TModelUnit x1, TModelUnit y1, TModelUnit x2, TModelUnit y2, const CRgbaColor &color, bool border=false) const

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

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

void DrawRect(const TModelRect &rc) 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 GetMaxLabelWidth(const CGlBitmapFont &font) const

In screen pixel..

void DrawPartialBar(TModelUnit x1, TModelUnit y1, TModelUnit x2, TModelUnit y2, bool p_start, bool p_stop, bool loc) 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.

TSeqPos GetVisSeqFrom() const

const CRgbaColor & GetSelLabelColor() const

bool WillLabelFit(const TModelRect &rc) const

void DrawSquare(const TModelPoint &p, TModelUnit size, const CRgbaColor &color, bool neg_strand) const

void Draw3DArrow(const TModelPoint &p, TModelUnit size, bool neg_strand) const

void Draw3DQuad(TModelUnit x1, TModelUnit y1, TModelUnit x2, TModelUnit y2, const CRgbaColor &color, bool border=false) const

void SetIsDrawn(const string &sPName, bool isDrawn)

void Draw3DTriangle(const TModelPoint &p, TModelUnit size, const CRgbaColor &color, bool neg_strand, bool need_neck) const

void DrawBackground(const TModelRect &rcm, TModelUnit border) const

void DrawStrandIndicators(const TModelPoint &start, TModelUnit length, TModelUnit apart, TModelUnit size, const CRgbaColor &color, bool neg_strand, bool avoid_center=false, bool single_indicator_center=false, const vector< TModelRange > *labels_ranges=nullptr) const

class CRgbaColor provides a simple abstraction for managing colors.

CRuler is a renderable object drawing a scale with position labels.

void SetTextLabel(const string &label)

void SetFont(CGlTextureFont::EFontFace font_type, unsigned int font_size=12)

void SetBaseWidth(int value)

@ eOppLabelTickHeight

tick size at label position (opposite)

@ eOppMajorTickHeight

major tick on the opposite side

@ eOppMinorTickHeight

minor tick on the opposite side

@ eLabelTickHeight

tick size at label position

void SetHorizontal(bool b_horz, ELabelPlacement place=eDefault, ELabelAlign aln=eAln_Center)

void SetDisplayOptions(int options)

virtual void Render(CGlPane &pane)

void SetGeometryParam(EGeometryParam geom, int value)

void SetMapping(const TAlignColl &coll)

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)

TSeqPos GetSequenceLength() const

const objects::CSeqVector & GetSeqVector(void) const

class CSeqGlyph defines an interface that wraps a rectilinear abstract object.

string GetTearlineText() const

ENeighbours m_Neighbours

Indicates whether the glyph has neighbours.

void x_InitHTMLActiveArea(CHTMLActiveArea &area) const

initialize the basic information for a given active area.

CRenderingContext * m_Context

the rendering context

virtual void x_OnLayoutChanged()

update the layout.

virtual void SetHeight(TModelUnit h)

const CRenderingContext * GetRenderingContext() const

Get the rendering context.

virtual TModelUnit GetRight() const

void x_DrawInnerLabels(TModelUnit base, const string &label, const CRgbaColor &color, const CGlTextureFont &font, bool side_label_visible, bool inside_only, vector< TModelRange > *labels_ranges=nullptr, TSeqRange *interval=nullptr, bool XOR_mode=false) const

bool IsInHor(TModelUnit x) const

void x_DrawException() const

Draw a shading background to indicate exception.

virtual void SetWidth(TModelUnit w)

CSeqGlyph * m_Parent

parent/child relationships for this feature

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.

virtual void SetTop(TModelUnit b)

virtual bool SetSelected(bool flag)

Select or deselect this glyph.

void x_Local2World(TModelPoint &p) const

Transform the coordiantes from local coord. to world coord.

virtual TModelUnit GetWidth() const

virtual TModelUnit GetLeft() const

TModelRect GetModelRect() const

get the bounding box.

vector< CHTMLActiveArea > TAreaVector

const CSeqGlyph * GetParent(void) const

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

namespace ncbi::objects::

const string & GetNamedQual(const CTempString &qual_name) const

Return a named qualifier.

Seq-loc iterator class – iterates all intervals from a seq-loc in the correct order.

Seq-loc iterator class – iterates all intervals from a seq-loc in the correct order.

bool IsDeletionInsertion() const

bool IsTranslocation() const

virtual bool IsNegativeStrand(TNumrow row) const =0

vector< TSeqRange > TIntervals

virtual IAlnExplorer::TNumrow GetAnchor() const =0

static CConstRef< CDbtag > GetTag(const CSeq_feat &SrcFeat)

find a SNP tag in the feature returns NULL if no such tag (sm_dbTag_dbSNP)

vector< string > TAlleles

list of alleles belonging to particular SNP a deletion is represented by a "-"

static void GetAlleles(const CMappedFeat &mapped_feat, TAlleles &Alleles)

Return list of alleles encoded in qual.

const_iterator end() const

const_iterator find(const key_type &key) const

static const Colors colors

int GetSubtype(CFieldNamePanel *field_name_panel, string &ncRNA_class)

static const float kMinScaleForRulerLabels

Shoudl match feature_ds.cpp::kMinScaleForMapping i.e.

static const TModelUnit kRSiteMarkerThreshold

Restriction sites marker visibility threshold (ie if the marker's width is smaller then the threshold...

static const int kVertSpace

vertical space between elements.

static const TModelUnit kRSiteMarkerWidth

Restriction sites marker width (absolute)

static int s_GetLiteralLength(const CVariation_ref &var)

TVPUnit s_AdjustScreenCoordinate(TModelUnit x)

static const int kRulerHeight

feature ruler height.

static const TModelUnit kRSiteMarkerHeight

Restriction sites marker height (relative to the height of the bar)

bool Empty(const CNcbiOstrstream &src)

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 REVERSE_ITERATE(Type, Var, Cont)

ITERATE macro to reverse sequence through container elements.

#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)

static bool IsException(const objects::CSeq_feat &feat)

static bool IsPartialStart(const objects::CSeq_loc &loc)

static bool IsPartialFeature(const objects::CSeq_feat &feat)

static bool IsPseudoFeature(const objects::CSeq_feat &feat)

static bool IsPartialStop(const objects::CSeq_loc &loc)

static bool IsSameStrands(const objects::CSeq_loc &loc)

static bool isRmtAnnotName(const string &sAnnotname)

check if a given annotation was created by a remote file pipeline

vector< TMappedInt > TMappingInfo

void SetModelLimitsRect(const TModelRect &R)

void SetViewport(const TVPRect &R)

virtual void Enable(GLenum glstate)=0

virtual void LineStipple(GLint factor, GLushort pattern)=0

Set line stipple pattern: glLineStipple(). Deprecated in gl 3.2+.

void Color3f(GLfloat r, GLfloat g, GLfloat b)

IRender & GetGl()

convenience function for getting current render manager

TVPRect & GetViewport(void)

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

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

virtual void LoadIdentity()=0

TVPUnit ProjectY(TModelUnit m_y) const

virtual void PopMatrix()=0

CRange< TModelUnit > TModelRange

void SetVisibleRect(const TModelRect &R)

virtual TModelUnit TextWidth(const char *text) const

Compute and return font metrics.

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()

void SetHorz(T left, T right)

CGlPoint< TModelUnit > TModelPoint

virtual void ColorC(const CRgbaColor &c)=0

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

virtual void PushMatrix()=0

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

Truncate text to the secified width.

@ eFontFace_Helvetica_Bold

CRgbaColor ContrastingColor(bool onlyBW=true) const

Return a color guaranteed to contrast nicely with this color.

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

void SetLocation(const objects::CSeq_loc &loc)

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

set the color from an Fl_Color

static NSnp::TClinSigID ClinSigFromString(const string &clinsig)

converts string to clinical significance type (CPhenotype::EClinical_significance)

float GetBlue(void) const

float GetGreen(void) const

static CIRef< ITooltipFormatter > CreateTooltipFormatter(ETooltipFormatters)

factory for requested tooltip formatter creation

void FromString(const string &str)

Assign color values encoded in a string.

void SetTaxId(int tax_id)

void Lighten(float scale)

static bool GetClinSigValue(const CSeq_feat &ref, string &attr_value)

returns CLNSIG attribute value from VcfAttribute user object returns false if not found

static bool isFromVcf(const CSeq_feat &variation_ref)

void SetMappingInfo(const CSeqUtils::TMappingInfo &mapping_info)

static CVariation_inst::EType GetVcfType(const CSeq_feat &variation_ref)

void SetMappedFeat(const objects::CMappedFeat &mapped_feat)

static void ClinSigAsColor(NSnp::TClinSigID ClinSigID, CRgbaColor &color)

returns color for clinsig values (SV-4908) returns #767677 for undefined values

float GetRed(void) const

Get specific channels in floating point values.

@ eTooltipFormatter_CSSTable

generated table is CSS based, generated NCBI URLs are paths (recommended for SViewer)

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

Optimized implementation of CSerialObject::Assign, which is not so efficient.

CConstRef< CSeq_id > GetSeqId(void) const

string AsString(void) const

@ eContent

Untagged human-readable accession or the like.

CRef< CSeq_loc > MakeSeq_loc(EMakeType make_type=eMake_CompactType) const

return constructed CSeq_loc with all changes

void SetPacked_int(TPacked_int &v)

void SetFrom(TSeqPos from)

Set the range from position.

void SetTo(TSeqPos to)

Set the range to position.

ENa_strand GetStrand(void) const

Get the location's strand.

bool IsReverseStrand(void) const

Return true if all ranges have reverse strand.

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

CConstRef< CSeq_loc > GetRangeAsSeq_loc(void) const

Get seq-loc for the current iterator position.

bool IsSetStrand(void) const

Get strand.

bool IsEmpty(void) const

True if the current location is empty.

const CSeq_id * GetId(void) const

Get the id of the location return NULL if has multiple ids or no id at all.

TRange GetRange(void) const

Get the range.

ENa_strand GetStrand(void) const

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.

ENa_strand GetStrand(const CSeq_loc &loc, CScope *scope=0)

Returns eNa_strand_unknown if multiple Bioseqs in loc Returns eNa_strand_other if multiple strands in...

TTaxId GetTaxId(const CBioseq_Handle &handle)

return the tax-id associated with a given sequence.

@ eGetId_ForceGi

return only a gi-based seq-id

CBioseq_Handle GetBioseqHandle(const CSeq_id &id)

Get bioseq handle by seq-id.

@ 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).

bool Empty(void) const THROWS_NONE

Check if CConstRef is empty – not pointing to any object which means having a null value.

TObjectType * GetPointer(void) const THROWS_NONE

Get pointer,.

CRef< C > Ref(C *object)

Helper functions to get CRef<> and CConstRef<> objects.

TObjectType * GetPointer(void) THROWS_NONE

Get pointer,.

void Reset(void)

Reset reference object.

void Reset(void)

Reset reference object.

int64_t Int8

8-byte (64-bit) signed integer

position_type GetLength(void) const

bool AbuttingWith(const TThisType &r) const

bool IntersectingWith(const TThisType &r) const

TThisType & CombineWith(const TThisType &r)

TThisType IntersectionWith(const TThisType &r) const

position_type GetToOpen(void) const

TThisType & Set(position_type from, position_type to)

#define END_NCBI_SCOPE

End previously defined NCBI scope.

#define BEGIN_NCBI_SCOPE

Define ncbi namespace.

static SIZE_TYPE FindNoCase(const CTempString str, const CTempString pattern, SIZE_TYPE start, SIZE_TYPE end, EOccurrence which=eFirst)

Find the pattern in the specified range of a string using a case insensitive search.

static double StringToDouble(const CTempStringEx str, TStringToNumFlags flags=0)

Convert string to double.

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

Convert int to string.

static string Join(const TContainer &arr, const CTempString &delim)

Join strings using the specified delimiter.

static string & Replace(const string &src, const string &search, const string &replace, string &dst, SIZE_TYPE start_pos=0, SIZE_TYPE max_replace=0, SIZE_TYPE *num_replace=0)

Replace occurrences of a substring within a string.

static bool EqualNocase(const CTempString s1, SIZE_TYPE pos, SIZE_TYPE n, const char *s2)

Case-insensitive equality of a substring with another string.

static enable_if< is_arithmetic< TNumeric >::value||is_convertible< TNumeric, Int8 >::value, string >::type NumericToString(TNumeric value, TNumToStringFlags flags=0, int base=10)

Convert numeric value to string.

static string & ReplaceInPlace(string &src, const string &search, const string &replace, SIZE_TYPE start_pos=0, SIZE_TYPE max_replace=0, SIZE_TYPE *num_replace=0)

Replace occurrences of a substring within a string.

@ eNocase

Case insensitive compare.

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.

bool IsStr(void) const

Check if variant Str is selected.

bool IsLim(void) const

Check if variant Lim is selected.

const TTag & GetTag(void) const

Get the Tag member data.

bool IsId(void) const

Check if variant Id is selected.

const TDb & GetDb(void) const

Get the Db member data.

TLim GetLim(void) const

Get the variant data.

TMin GetMin(void) const

Get the Min member data.

const TStr & GetStr(void) const

Get the variant data.

bool IsRange(void) const

Check if variant Range is selected.

TMax GetMax(void) const

Get the Max member data.

TId GetId(void) const

Get the variant data.

const TRange & GetRange(void) const

Get the variant data.

@ eLim_tl

space to left of position

E_Choice Which(void) const

Which variant is currently selected.

const TIds & GetIds(void) const

Get the Ids member data.

list< CRef< CUser_object > > TExts

E_Choice Which(void) const

Which variant is currently selected.

const TId & GetId(void) const

Get the Id member data.

const TLocal & GetLocal(void) const

Get the variant data.

TFrame GetFrame(void) const

Get the Frame member data.

const TData & GetData(void) const

Get the Data member data.

const TGeneral & GetGeneral(void) const

Get the variant data.

const TGiim & GetGiim(void) const

Get the variant data.

bool IsSetIds(void) const

set of Ids; will replace 'id' field Check if a value has been assigned to Ids data member.

bool IsSetId(void) const

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

TGibb GetGibb(void) const

Get the variant data.

const TVariation & GetVariation(void) const

Get the variant data.

bool IsSetFrame(void) const

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

@ e_General

for use by various databases

@ e_Gibb

geninfo backbone

@ e_Local

for local software use

@ eFrame_three

reading frame

const TFuzz_from & GetFuzz_from(void) const

Get the Fuzz_from member data.

TId GetId(void) const

Get the Id member data.

bool IsMix(void) const

Check if variant Mix is selected.

ENa_strand

strand of nucleic acid

const Tdata & Get(void) const

Get the member data.

const TPnt & GetPnt(void) const

Get the variant data.

TPoint GetPoint(void) const

Get the Point member data.

const TFuzz_to & GetFuzz_to(void) const

Get the Fuzz_to member data.

const TFuzz & GetFuzz(void) const

Get the Fuzz member data.

TStrand GetStrand(void) const

Get the Strand member data.

const Tdata & Get(void) const

Get the member data.

bool CanGetFuzz(void) const

Check if it is safe to call GetFuzz method.

bool CanGetStrand(void) const

Check if it is safe to call GetStrand method.

bool IsPacked_int(void) const

Check if variant Packed_int is selected.

bool CanGetPoint(void) const

Check if it is safe to call GetPoint method.

bool IsSetFuzz_to(void) const

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

bool IsInt(void) const

Check if variant Int is selected.

const TInt & GetInt(void) const

Get the variant data.

bool IsSetFuzz_from(void) const

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

const TMix & GetMix(void) const

Get the variant data.

bool IsPnt(void) const

Check if variant Pnt is selected.

const TPacked_int & GetPacked_int(void) const

Get the variant data.

@ eNa_strand_both_rev

in reverse orientation

@ eNa_strand_both

in forward orientation

const TInstance & GetInstance(void) const

Get the variant data.

bool IsSetDelta(void) const

Sequence that replaces the location, in biological order.

const TId & GetId(void) const

Get the Id member data.

const TDelta & GetDelta(void) const

Get the Delta member data.

const TData & GetData(void) const

Get the Data member data.

bool IsInstance(void) const

Check if variant Instance is selected.

list< CRef< CDelta_item > > TDelta

bool CanGetId(void) const

Check if it is safe to call GetId method.

@ eType_snv

delta=[morph of length 1] NOTE: this is snV not snP; the latter requires frequency-based validation t...

@ eType_mnp

delta=[morph of length >1]

@ eType_delins

delta=[del, ins]

bm::gap_word_t gap_length(const bm::gap_word_t *buf) noexcept

Returs GAP block length.

static void text(MDB_val *v)

constexpr auto sort(_Init &&init)

constexpr auto front(list< Head, As... >, T=T()) noexcept -> Head

constexpr bool empty(list< Ts... >) noexcept

Int4 delta(size_t dimension_, const Int4 *score_)

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

static bool GetIds(const T &d, set< string > &labels, const string name="", bool detect=false, bool found=false)

string GetProduct(const CProt_ref &prot_ref)

static const sljit_gpr r1

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

static const sljit_gpr r0

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

sorting functor for finding a range inside a collection of layout objects

bool operator()(const CRef< CLayoutObject > &obj1, const CRef< CLayoutObject > &obj2) const

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