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NCBI C++ ToolKit: src/algo/gnomon/gnomon_seq.cpp Source File

*

=

;

= src.size();

(

= 0;

<

; ++

)

= src.size();

(

= 0;

<

; ++

)

dst.push_back(

(src[

]) );

<

Res>

<

Res>

Res * start_codon;

(strand ==

)

equal(start_codon,start_codon+3,seq);

<

Res>

(strand ==

) {

(

= 1;

<= 3; ++

)

(

= 1;

<= 3; ++

)

(CEResidueVec::const_iterator pos = mrna.begin()+search_region.

(); (pos = search(pos,mrna.end(),codon,codon+3)) < mrna.begin()+search_region.

(); ++pos) {

= (

)(pos-mrna.begin());

(fixed_frame==-1 || fixed_frame==frame)

positions[frame].push_back(

);

(

=1;

<=3; ++

)

(

= 0;

< 3; ++

)

(stops[

].begin(), stops[

].end());

codon_start = start+frame-3;

(codon_start >= 0 &&

(&seq_strand[codon_start]))

left_cds_limit = -1;

reading_frame_start = (

)mrna.size();

reading_frame_stop = (

)mrna.size();

right_cds_limit = (

)mrna.size();

reading_frame_start = rf.

();

(reading_frame_start >= 0);

reading_frame_stop = rf.

();

(reading_frame_stop >= 0);

(reading_frame_start == 0 &&

(&mrna[reading_frame_start]) && reading_frame_start+3 < reading_frame_stop)

reading_frame_start += 3;

( -1 <= left_cds_limit && left_cds_limit <= reading_frame_start );

( 0 <= reading_frame_start && reading_frame_start <= reading_frame_stop && reading_frame_stop <

(mrna.size()) );

( reading_frame_stop <= right_cds_limit && right_cds_limit <=

(mrna.size()) );

frame = reading_frame_start%3;

(left_cds_limit<0) {

(reading_frame_start >= 3) {

(stops[frame].

()>0)

left_cds_limit = stops[frame].back()+3;

reading_frame_start = reading_frame_stop-5;

reading_frame_start =

(protrf.

(),reading_frame_start);

(left_cds_limit<0) {

starts[0].push_back(-3);

model_start = (

)contig_seq.size()-1-model_start;

(

= 0;

<3; ++

) {

(frame == -1 || frame ==

) {

stops[

].push_back(

-3);

starts[

].push_back(

-3);

(obeystart && model.

()) {

starts[frame].push_back(start.

());

}

(reading_frame_start-left_cds_limit >= 3) {

}

(right_cds_limit - reading_frame_stop >= 3) {

(

(mrna.size()) <= right_cds_limit) {

stops[mrna.size()%3].push_back((

)mrna.size());

stops[(mrna.size()-1)%3].push_back((

)mrna.size()-1);

stops[(mrna.size()-2)%3].push_back((

)mrna.size()-2);

vector<int>::const_iterator it_stop = lower_bound(stops.begin(),stops.end(),start);

(it_stop != stops.begin()) {

it_start = lower_bound(starts.begin(), starts.end(), stop);

(it_start != starts.end()) {

(!fs_only ||

%3 != 0)

left_type,

right_type,

& left_edit_extra_seq,

& right_edit_extra_seq)

((

)left_edit_extra_seq.length() == 0 || (

)left_edit_extra_seq.length() == left_edite);

((

)right_edit_extra_seq.length() == 0 || (

)right_edit_extra_seq.length() == right_edite);

TInDels::const_iterator fsi_end,

type_a,

type_b,

& gseq_a,

& gseq_b)

TInDels::const_iterator fsi = fsi_begin;

( ;fsi != fsi_end && fsi->Loc() < orig_a; ++fsi ) {

( !fsi->IntersectingWith(orig_a,orig_b) );

left_edit_extra_seq = gseq_a;

( ;fsi != fsi_end && fsi->Loc() == orig_a && !fsi->IsMismatch(); ++fsi ) {

(fsi->IsInsertion()) {

orig_a += fsi->Len();

left_orige += fsi->Len();

edit_a += fsi->Len();

left_edite += fsi->Len();

left_edit_extra_seq += fsi->GetInDelV();

( ; fsi != fsi_end && fsi->IsMismatch() && fsi->Loc() == orig_a+(

)mism.size(); ++fsi)

mism += fsi->GetInDelV();

(fsi != fsi_end && fsi->InDelEnd() <= orig_b+1) {

right_edit_extra_seq;

( ;fsi != fsi_end && fsi->Loc() ==

&& !fsi->IsMismatch(); ++fsi ) {

(fsi->IsInsertion()) {

right_orige += fsi->Len();

right_edite += fsi->Len();

right_edit_extra_seq += fsi->GetInDelV();

(next_orig_a > orig_b) {

right_edit_extra_seq += gseq_b;

right_edite += gseq_b.length();

(orig_a, edit_a,

, mism, left_orige, left_edite, right_orige, right_edite, type_a, tb, left_edit_extra_seq, right_edit_extra_seq);

orig_a = next_orig_a;

edit_a +=

+right_edite;

left_orige = right_orige;

left_edite = right_edite;

left_edit_extra_seq = right_edit_extra_seq;

( ; fsi != fsi_end && fsi->IsMismatch() && fsi->Loc() == orig_a+(

)mism.size(); ++fsi)

mism += fsi->GetInDelV();

right_edit_extra_seq;

(orig_a+

> orig_b) {

right_edit_extra_seq = gseq_b;

(orig_a, edit_a,

, mism, left_orige, left_edite, 0, (

)gseq_b.length(), type_a, tb, left_edit_extra_seq, right_edit_extra_seq);

left_edit_extra_seq.clear();

(orig_a <= orig_b) {

= orig_b-orig_a+1;

(orig_a, edit_a,

, mism, left_orige, left_edite, 0, (

)gseq_b.length(), type_a, type_b, left_edit_extra_seq, gseq_b);

(transcript_exons.size() == exons.size());

(transcript_exons.size() == 1 || (orientation ==

&& transcript_exons.front().GetFrom() < transcript_exons.back().GetFrom()) ||

(orientation ==

&& transcript_exons.front().GetFrom() > transcript_exons.back().GetFrom()));

(

= 0;

< exons.size(); ++

) {

diff += exonlen-(transcript_exons[

].GetTo()-transcript_exons[

].GetFrom()+1);

(!

->IsMismatch())

diff += (

->IsDeletion()) ?

->Len() : -

->Len();

(

= 0;

< exons.size(); ++

) {

(exons[

].Limits().Empty()) {

(

== 0 || exons[

-1].Limits().NotEmpty());

(

== exons.size()-1 || exons[

+1].Limits().NotEmpty());

(

> 0 && exons[

-1].Limits().

()) {

gseq_a = exons[

-1].m_seq;

estart += gseq_a.length();

(

< exons.size()-1 && exons[

+1].Limits().Empty()) {

gseq_b = exons[

+1].m_seq;

estart =

(exons[

].GetFrom(), exons[

].GetTo(), estart, indels.begin(), indels.end(), type_a, type_b, gseq_a, gseq_b);

(

!= exons.size()-1) {

estart += transcript_exons[

+1].GetFrom()-transcript_exons[

].GetTo()-1;

estart += transcript_exons[

].GetFrom()-transcript_exons[

+1].GetTo()-1;

TInDels::const_iterator fsi_begin = indels.begin();

TInDels::const_iterator fsi_end = indels.end();

(

= 0;

< exons.size(); ++

) {

(exons[

].Limits().

()) {

(

== 0 || exons[

-1].Limits().NotEmpty());

(

== exons.size()-1 || exons[

+1].Limits().NotEmpty());

(

> 0 && exons[

-1].Limits().

()) {

gseq_a = exons[

-1].m_seq;

estart += gseq_a.length();

(

< exons.size()-1 && exons[

+1].Limits().Empty()) {

gseq_b = exons[

+1].m_seq;

(stop < lim.

())

;

(lim.

() < start)

;

(lim.

() >= start) {

(lim.

() <= stop) {

stop = lim.

();

(

!= exons.size()-1 && (!exons[

+1].m_fsplice || !exons[

].m_ssplice))

<

In,

Out>

edited_sequence.clear();

s.insert(s.end(),

,

);

(

=

;

<

; ++

)

edited_sequence.push_back(original_sequence[

]);

seq.insert(seq.end(),

,

);

seq.insert(seq.end(),

,

);

CAlignMap::EditedSequence<CResidueVec,CResidueVec>(

& original_sequence,

& edited_sequence,

includeholes)

;

CAlignMap::EditedSequence<CEResidueVec,CEResidueVec>(

& original_sequence,

& edited_sequence,

includeholes)

;

CAlignMap::EditedSequence<string,string>(

& original_sequence,

& edited_sequence,

includeholes)

;

CAlignMap::EditedSequence<CAlignCollapser::CPartialString,string>(

& original_sequence,

& edited_sequence,

includeholes)

;

(snap_to_codons) {

snapped =

;

(snap_to_codons) {

snapped =

;

(p <

.front().GetExtendedFrom() || p >

.back().GetExtendedTo())

-1;

(p <

.front().GetFrom()) {

(move_mode ==

&&

.front().GetTypeFrom() !=

) {

.front().GetExtendedFrom();

(p >

.back().GetTo()) {

.back().GetExtendedTo();

(p >

[num].GetTo()) {

(

[num].GetTypeTo() ==

)

[num+1].GetExtendedFrom();

[num].GetExtendedTo();

}

(p ==

[num].GetTo()) {

[num].GetExtendedTo();

}

(p ==

[num].GetFrom() && move_mode ==

&&

[num].GetTypeFrom() !=

) {

[num].GetExtendedFrom();

[num].GetTo();

}

(p ==

[num].GetFrom()) {

[num].GetExtendedFrom();

[num].GetFrom();

[num].GetFrom()+p-

[num].GetFrom();

TSignedSeqPos FShiftedMove(TSignedSeqPos orig_pos, int len) const

static int FindLowerRange(const vector< CAlignMap::SMapRange > &a, TSignedSeqPos p)

TSignedSeqRange ShrinkToRealPointsOnEdited(TSignedSeqRange edited_range) const

void InsertOneToOneRange(TSignedSeqPos orig_start, TSignedSeqPos edited_start, TSignedSeqPos len, const string &mism, TSignedSeqPos left_orige, TSignedSeqPos left_edite, TSignedSeqPos right_orige, TSignedSeqPos right_edite, EEdgeType left_type, EEdgeType right_type, const string &left_edit_extra_seq, const string &right_edit_extra_seq)

static TSignedSeqRange MapRangeAtoB(const vector< CAlignMap::SMapRange > &a, const vector< CAlignMap::SMapRange > &b, TSignedSeqRange r, ERangeEnd lend, ERangeEnd rend)

vector< SMapRange > m_edited_ranges

TSignedSeqPos InsertIndelRangesForInterval(TSignedSeqPos orig_a, TSignedSeqPos orig_b, TSignedSeqPos edit_a, TInDels::const_iterator fsi_begin, TInDels::const_iterator fsi_end, EEdgeType type_a, EEdgeType type_b, const string &gseq_a, const string &gseq_b)

TSignedSeqRange MapRangeEditedToOrig(TSignedSeqRange edited_range, bool withextras=true) const

TSignedSeqPos MapOrigToEdited(TSignedSeqPos orig_pos) const

void EditedSequence(const In &original_sequence, Out &edited_sequence, bool includeholes=false) const

TSignedSeqPos MapEditedToOrig(TSignedSeqPos edited_pos) const

TSignedSeqRange ShrinkToRealPoints(TSignedSeqRange orig_range, bool snap_to_codons=false) const

int FShiftedLen(TSignedSeqRange ab, ERangeEnd lend, ERangeEnd rend) const

static TSignedSeqPos MapAtoB(const vector< CAlignMap::SMapRange > &a, const vector< CAlignMap::SMapRange > &b, TSignedSeqPos p, ERangeEnd move_mode)

TSignedSeqRange MapRangeOrigToEdited(TSignedSeqRange orig_range, ERangeEnd lend, ERangeEnd rend) const

vector< SMapRange > m_orig_ranges

TSignedSeqRange Start() const

TSignedSeqRange ProtReadingFrame() const

TSignedSeqRange ReadingFrame() const

const CCDSInfo & GetCdsInfo() const

vector< CModelExon > TExons

static EResidue _fromACGT(TResidue x)

static const EResidue * _rev_codons(int i)

static const EResidue * _codons(int i)

static const Res * _rev_codons(int i)

static const Res * _codons(int i)

static Res _fromACGT(TResidue x)

bool Empty(const CNcbiOstrstream &src)

vector< TResidue > CResidueVec

bool Include(TSignedSeqRange big, TSignedSeqRange small)

vector< CInDelInfo > TInDels

objects::CSeqVectorTypes::TResidue TResidue

bool IsStopCodon(const Res *seq, int strand)

bool FindFirstStart(const vector< int > &starts, int stop, int &start)

bool FindUpstreamStop(const vector< int > &stops, int start, int &stop)

static const EResidue s_ecodons2[3]

const TResidue rev_codons[4][4]

const TResidue codons[4][4]

void FindAllStops(TIVec stops[], const CEResidueVec &mrna, TSignedSeqRange search_region, int fixed_frame)

const char *const k_aa_table

void FindStartsStops(const CGeneModel &model, const CEResidueVec &contig_seq, const CEResidueVec &mrna, const CAlignMap &mrnamap, TIVec starts[3], TIVec stops[3], int &frame, bool obeystart)

const EResidue k_toMinus[5]

void FindAllCodonInstances(TIVec positions[], const EResidue codon[], const CEResidueVec &mrna, TSignedSeqRange search_region, int fixed_frame)

const EResidue * ecodons[4]

static const EResidue s_ecodons0r[3]

static const EResidue s_ecodons1[3]

static const EResidue s_ecodons2r[3]

template bool IsStartCodon< TResidue >(const TResidue *seq, int strand)

const EResidue * rev_ecodons[4]

template bool IsStartCodon< EResidue >(const EResidue *seq, int strand)

void ReverseComplement(const CEResidueVec &src, CEResidueVec &dst)

bool IsStartCodon(const Res *seq, int strand)

template bool IsStopCodon< EResidue >(const EResidue *seq, int strand)

void Convert(const CResidueVec &src, CEResidueVec &dst)

template bool IsStopCodon< TResidue >(const TResidue *seq, int strand)

static const EResidue s_ecodons3r[3]

bool Partial5pCodonIsStop(const CEResidueVec &seq_strand, int start, int frame)

static const EResidue s_ecodons3[3]

void PushInDel(TInDels &indels, bool fs_only, TSignedSeqPos p, int len, CInDelInfo::EType type, const string &seq="")

void FindAllStarts(TIVec starts[], const CEResidueVec &mrna, TSignedSeqRange search_region, int fixed_frame)

static const EResidue s_ecodons0[3]

static const EResidue s_ecodons1r[3]

TResidue toACGT(EResidue c)

EResidue fromACGT(TResidue c)

#define ITERATE(Type, Var, Cont)

ITERATE macro to sequence through container elements.

int TSignedSeqPos

Type for signed sequence position.

position_type GetLength(void) const

bool NotEmpty(void) const

static TThisType GetEmpty(void)

static position_type GetWholeFrom(void)

CRange< TSignedSeqPos > TSignedSeqRange

static position_type GetWholeTo(void)

#define END_NCBI_SCOPE

End previously defined NCBI scope.

#define END_SCOPE(ns)

End the previously defined scope.

#define BEGIN_NCBI_SCOPE

Define ncbi namespace.

#define BEGIN_SCOPE(ns)

Define a new scope.

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.

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_)

void Out(T t, int w, CNcbiOstream &to=cout)

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

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