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

prot_seq, trans_seq;

prot_seq = trans_seq;

ifrom = lit.GetRange().GetFrom();

ito = lit.GetRange().GetTo();

basesIN[2], basesOUT[2];

(

pos = neg ? ito : ifrom;

(neg ? (pos -

>= ifrom) : (pos +

<= ito)) &&

idx != prot_seq.length() && idx != trans_seq.length() ;

(neg ? pos -= 3 : pos += 3), ++idx)

mismatch = (prot_seq[idx] != trans_seq[idx]);

basesIN [0] = prot_seq[idx];

basesOUT[0] = trans_seq[idx];

seq_start + 0.5, trans_y,

);

main_seq, tmp_seq;

vec.

(seq_start - 1, seq_start + 2, tmp_seq);

0,

(tmp_seq.length()), main_seq);

reverse(main_seq.begin(), main_seq.end());

seq_start + 0.5, gen_y,

);

diff = neg ? seq_start - ifrom : ito - seq_start;

}

(diff == 1) {

}

(diff == 0) {

will_fit =

;

base_width = aln_mgr->

(aln_mgr->GetAnchor());

(will_fit &&

().IsSetExcept() &&

().HasExceptionText(

))

prot_len = prot_vec.

();

gen_len = prot_len * 3;

(cds_seq.empty()) {

&

().GetData().GetCdregion().GetCode() :

;

(cds_seq.empty()) {

gen_len =

().GetTotalRange().GetLength();

prot_len = gen_len / 3 + 1;

&

().GetData().GetCdregion().GetCode() :

;

(prot_seq.empty())

prot_seq = trans_seq;

aligned_seq = aln_mgr->GetQuery();

base_width = aln_mgr->GetBaseWidth(anchor);

anchor_step = base_width == 3 ? 1 : 3;

codon_mismatch_col(

);

translated_col(

);

aligned_neg = aln_mgr->IsNegativeStrand(aligned_seq);

anchor_neg = aln_mgr->IsNegativeStrand(anchor);

& anchor_range = map_it.m_AnchorRange;

& prod_int = *map_it.m_ProductInt;

& gen_int = *map_it.m_MappedInt;

& prod_range = map_it.m_MappedProdRange;

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

;

aln_strand = anchor_neg || aligned_neg;

anchor_sign = (aln_strand && neg || !aln_strand && !neg) ? 1 : -1;

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

prod_pos = prod_int.GetFrom();

prod_stop = prod_int.GetTo() + 1;

prod_stop = min<int>(prod_stop, prod_pos +

(

(gen_range.

()) / base_width));

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

prod_from = prod_range.GetFrom();

frame = prod_from > 0 ? prod_from % 3 : prot_offset;

prod_pos_f1 = (prod_from / 3) * 3 + 1;

pos += ((anchor_sign * anchor_step) / 3) * (prod_pos_f1 - prod_from);

pos += (anchor_sign * anchor_step);

(prod_pos < prod_stop) {

(prod_pos >= prot_seq.size())

(anchor_sign > 0 && pos > (

)anchor_range.GetTo())

(anchor_sign < 0 && pos < (

)anchor_range.GetFrom())

(prod_pos < prot_seq.size())

prot_in[0] = prot_seq[prod_pos];

(prod_pos < trans_seq.size())

prot_out[0] = trans_seq[prod_pos];

mismatch = (prot_in[0] != prot_out[0]);

pos + 0.5, prot_y,

);

p = prod_pos > 0 ? (prod_pos * 3) : 0;

codon = cds_seq.substr(p, 3);

gen_codon = gen_seq.substr(p, 3);

(codon, pos, gen_y, flip_strand != (anchor_sign < 0),

);

gl.

(translated_col);

pos += anchor_sign * anchor_step;

prot_len = prot_vec.

();

cerr <<

<< endl << prot_seq << endl <<

<<

prot_seq.length() <<

<< prot_seq.length() * 3 << endl;

gen_len = prot_len * 3;

cerr <<

<< endl <<

<< *sfp << endl;

cerr <<

<< endl << cds_seq << endl <<

<< cds_seq.length() <<

gen_len =

().GetTotalRange().GetLength();

prot_len = gen_len / 3 + 1;

cerr <<

<< endl;

gen_seq.reserve(gen_len);

f1 = iter.first->GetFrom();

f2 = iter.second->GetFrom();

t2 = iter.second->GetTo();

gen_seq.append(f1 - pre_t1,

);

cerr <<

(f1 - pre_t1,

);

0,

(tmp_seq.length()), seq);

pre_t1 = iter.first->GetTo() + 1;

cerr << tmp_seq.length() <<

<< tmp_seq << endl;

cerr <<

<< endl << trans_seq << endl <<

<<

trans_seq.length() <<

<< trans_seq.length() * 3 << endl;

(prot_seq.empty())

prot_seq = trans_seq;

prot_in[2], prot_out[2];

codon_mismatch_col(

);

translated_col(

);

& prod_int = *map_it.first;

& gen_int = *map_it.second;

(

!= previous_prod_int) {

(previous_prod_int->

() != (prod_int.GetFrom() - 1)) {

prev_frame += prod_int.

() - previous_prod_int->

() - 1;

previous_prod_int = &prod_int;

cerr <<

<< prod_int.

() <<

<< prod_int.GetTo() <<

<< endl;

cerr <<

<< gen_int.GetFrom() <<

<< gen_int.GetTo() <<

<< endl;

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

;

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

step = neg ? -3 : 3;

(current_exon !=

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

()) {

(current_exon !=

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

()) {

frame = (gen_range.

() + prev_frame) % 3;

prod_pos = prod_int.GetFrom();

(prev_frame) {

c_pos += (neg ? -1 : 1);

c_pos += (neg ? 1 : -1);

prot_idx = (prod_pos > offs) ? (prod_pos - offs) / 3 : 0;

(prod_pos <= prod_stop) {

prot_in[0] = prot_out[0] =

;

(prot_idx < prot_seq.size())

prot_in[0] = prot_seq[prot_idx];

(prot_idx < trans_seq.size())

prot_out[0] = trans_seq[prot_idx];

mismatch = (prot_in[0] != prot_out[0]);

(prod_pos - 1 < gen_seq.size())

gen_codon = gen_seq.substr(prod_pos - 1, 3);

(prot_idx * 3 < cds_seq.size())

codon = cds_seq.substr(prot_idx * 3 + offs, 3);

(codon, c_pos, gen_y, flip_strand != neg,

);

gl.

(translated_col);

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

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

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

(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;

c_pos += (neg ? -1 : 1);

prev_gen.

(&gen_int);

prev_prod.

(&prod_int);

new_codon = codon_str;

= codon_str.size();

(

> 0 &&

< 5) {

(

) new_codon +=

;

new_codon.insert(0,

);

(neg) std::reverse(new_codon.begin(), new_codon.end());

pos + 0.5, y,

);

User-defined methods of the data storage class.

static const int kVertSpace

CRgbaColor m_SeqProtMismatch

mismatched sequence color.

CGlTextureFont m_ProdFont

CRgbaColor m_SeqProtTrans

translated sequence color.

CGlTextureFont m_TransFont

CRef< CCdsConfig > m_CdsConfig

void x_DrawProtSeqWithMapping(TModelUnit trans_y, TModelUnit gen_y, TModelUnit prot_y) const

void x_DrawProjectedProtSeq(TModelUnit trans_y, TModelUnit gen_y, TModelUnit prot_y) const

void x_PutCodon(const string &codon_str, TSeqPos pos, TModelUnit y, bool neg, bool append) const

virtual void x_Draw() const

The default renderer for this layout object.

CCdsGlyph(const objects::CMappedFeat &feat)

virtual void x_UpdateBoundingBox()

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

TSeqPos x_GetProtOffset() const

Returns protein translation offset.

virtual void x_Draw() const

The default renderer for this layout object.

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

TIntervals m_Intervals

intervals (like for features or alignments).

virtual void x_UpdateBoundingBox()

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

CConstRef< CFeatureParams > m_Config

All the configs needed for rendering a feature.

CProjectedMappingInfo m_ProjectedMappingInfo

const TMappingInfo & GetMappingInfo() const

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

access the position of this object.

bool x_IsProjected() const

const objects::CMappedFeat & GetMappedFeature(void) const

Access a new, fully remapped feature.

const objects::CSeq_feat & GetFeature(void) const

Access the original feature.

TModelUnit GetBarHeight(bool overview) const

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

const IAlnGraphicDataSource * GetAlignmentDataSource() const

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

CRef< CSGSequenceDS > GetSeqDS() const

bool IsInVisibleRange(TSeqPos pos) const

TModelRange IntersectVisible(const CSeqGlyph *obj) const

const TModelUnit & GetScale() const

bool IsFlippedStrand() const

bool WillSeqLetterFit() const

is it enougth space to sequence letters.

class CRgbaColor provides a simple abstraction for managing colors.

objects::CScope & GetScope(void) const

Get the scope from the handle.

const objects::CSeqVector & GetSeqVector(void) const

CRenderingContext * m_Context

the rendering context

virtual void SetHeight(TModelUnit h)

virtual TModelUnit GetTop() const

virtual TModelUnit GetHeight() const

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)

namespace ncbi::objects::

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

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

virtual IAlnExplorer::TNumrow GetAnchor() const =0

static void DLIST_NAME() append(DLIST_LIST_TYPE *list, DLIST_TYPE *item)

unsigned int TSeqPos

Type for sequence locations and lengths.

int TSignedSeqPos

Type for signed sequence position.

IRender & GetGl()

convenience function for getting current render manager

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

virtual TModelUnit GetMetric(const CGlTextureFont *font, IGlFont::EMetric metric, const char *text=NULL, int len=-1) const =0

Calls the standard font metric functions except for pdf in which case it first replaces any bitmap fo...

virtual void ColorC(const CRgbaColor &c)=0

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

#define MSerial_AsnText

I/O stream manipulators –.

TRange GetTotalRange(void) const

const CSeq_feat * GetCDSForProduct(const CBioseq &product, CScope *scope)

Get the encoding CDS feature of a given protein sequence.

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)

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).

void Reset(void)

Reset reference object.

position_type GetLength(void) const

#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.

const TLocation & GetLocation(void) const

Get the Location member data.

TFrame GetFrame(void) const

Get the Frame member data.

const TData & GetData(void) const

Get the Data member data.

const TCdregion & GetCdregion(void) const

Get the variant data.

bool IsSetFrame(void) const

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

TFrom GetFrom(void) const

Get the From member data.

TTo GetTo(void) const

Get the To member data.

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

Returs GAP block length.

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

static const float kSequenceLevel

string GetProduct(const CProt_ref &prot_ref)

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