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

indels = GetInDels(fs_only);

(

->IntersectingWith(

,

))

selected_indels.push_back( *

);

selected_indels;

(!

->IsMismatch())

selected_indels.push_back(*

);

TExons::const_iterator e =

().begin();

(

->IsMismatch() ||

->Len()%3 == 0)

( ;e !=

().end() && (e->Limits().Empty() || !

->IntersectingWith(e->GetFrom(),e->GetTo())); ++e);

(

->InDelEnd() > e->GetTo() && e !=

().end()) {

TInDels::const_iterator

=

;

=

->Len() + (

->GetType() ==

->GetType() ?

->Len() : -

->Len());

selected_indels.push_back(*

);

selected_indels;

(

().back().Limits().NotEmpty()) {

(

().front().Limits().NotEmpty()) {

(

().back().Limits().NotEmpty()) {

(

= (

)

().

()-1;

> 0; --

) {

(

()[

].m_fsplice &&

()[

-1].m_ssplice &&

()[

].m_fsplice_sig !=

&&

()[

-1].m_ssplice_sig !=

) {

(

= 0;

< (

)

().size()-1; ++

) {

(

()[

].m_ssplice &&

()[

+1].m_fsplice &&

()[

].m_ssplice_sig !=

&&

()[

+1].m_fsplice_sig !=

) {

> cds.

()+limit;

(it->m_fsplice_sig !=

)

(it->m_ssplice_sig !=

)

(

ie = 0; ie < (

)

().size(); ++ie) {

(

()[ie].Limits().Empty())

diff +=

()[ie].m_seq.size();

diff +=

()[ie].Limits().GetLength();

(

->IsDeletion())

(

->IsInsertion())

(

.Orientation() !=

.Strand())

vector<TSignedSeqRange> transcript_exons;

(

ie = 0; ie < (

)

().size(); ++ie) {

transcript_exons.push_back(texon);

;

(

.NotEmpty()) {

*s =

(mapper(*s,

), s->m_status);

new_cds_info = another_cds_info;

new_cds_info = *

;

*

= new_cds_info;

modified =

;

(

= 1;

<

().size(); ++

) {

hole = !

()[

-1].m_ssplice || !

()[

].m_fsplice;

intron =

()[

].GetFrom()-

()[

-1].GetTo()-1;

new_exons.back().m_ssplice =

()[

].m_ssplice;

new_exons.back().AddTo(

()[

].GetTo()-

()[

-1].GetTo());

loc =

()[

-1].GetTo() + 1 + (intron-

)/2;

new_exons.push_back(

()[

]);

(intersection.

())

()[

].m_ssplice_sig.clear();

()[

+1].m_fsplice=

;

()[

].m_fsplice_sig.clear();

()[

-1].m_ssplice=

;

()[

-1].m_ssplice=

;

()[

+1].m_fsplice=

;

cds_clip_limits &= clip_limits;

intersection =

().front().Limits() & clip_limits;

intersection =

().back().Limits() & clip_limits;

cds_clip_limits.

(intersection.

());

precise_cds_clip_limits += e->Limits() & cds_clip_limits;

cds_clip_limits = precise_cds_clip_limits;

( cds_clip_limits.

()) {

cds_clip_limits.

(

.GetTo());

(left_determinant, right_determinant);

(

& exon :

()) {

(exon.GetFrom() <= clip_limits.

()) {

exon.m_fsplice =

;

exon.m_fsplice_sig.clear();

(exon.GetTo() >= clip_limits.

()) {

exon.m_ssplice =

;

exon.m_ssplice_sig.clear();

exon.Limits() = clip;

().front().m_fsplice =

;

().back().m_ssplice =

;

() &= ~left_determinant;

() &= ~right_determinant;

TInDels::const_iterator indl =

.begin();

(CGeneModel::TExons::const_iterator e =

().begin(); e !=

().end() && indl !=

.end(); ++e) {

(e->Limits().Empty())

( ;indl !=

.end() && indl->InDelEnd() < (indl->IsDeletion() ? e->GetFrom() : e->GetFrom()+1); ++indl);

( ;indl !=

.end() && e->GetFrom() == left && indl->IsDeletion() && indl->Loc() == left; ++indl);

(indl !=

.end() && indl->Loc() < e->GetFrom()) {

extra = e->GetFrom()-indl->Loc();

( ; indl !=

.end() && indl->Loc() <= e->GetTo(); ++indl)

indels.push_back(*indl);

( ; indl !=

.end() && e->GetTo() != right && indl->IsDeletion() && indl->Loc() == e->GetTo()+1; ++indl)

indels.push_back(*indl);

(!indels.empty() && indels.back().InDelEnd() > e->GetTo()+1) {

(indels.back().IsMismatch());

extra = indels.back().InDelEnd()-e->GetTo()-1;

indels.back() =

(indels.back().Loc(),indels.back().Len()-extra,

,indels.back().GetInDelV().substr(0,indels.back().Len()-extra));

(

->IntersectingWith(

,

))

fshifts.push_back( *

);

(intersection==0 || intersection==

.GetLength() || intersection==alimits.

())

.IntersectingWith(alimits) &&

!= alimits;

pair<int, int> rslt(-1, -1);

last_exon =

.Exons().size()-1;

(last_exon == 0 ||

.Limits().GetFrom() == intersect.

())

(last_exon == 1)

aleft = intersect.

() >

.Exons()[0].GetTo() ? 1 : 0;

aleft = std::lower_bound(

.Exons().begin(),

.Exons().end(), intersect.

(), [](

& e,

p){ return e.GetTo() < p; })-

.Exons().begin();

(intersect.

() <

.Exons()[aleft].GetFrom())

(aleft == last_exon ||

.Limits().GetTo() == intersect.

())

(aleft == last_exon-1)

aright = intersect.

() >

.Exons()[aleft].GetTo() ? last_exon : aleft;

aright = std::lower_bound(

.Exons().begin()+aleft,

.Exons().end(), intersect.

(), [](

& e,

p){ return e.GetTo() < p; })-

.Exons().begin();

(intersect.

() <

.Exons()[aright].GetFrom())

rslt.second = aright;

(

.Strand() !=

.Strand())

aflex =

;

bflex =

;

(intersect.

() < min_overlap)

aright = rslt.second;

bright = rslt.second;

(aright-aleft != bright-bleft)

(

ea = aleft, eb = bleft; ea < aright; ++ea, ++eb) {

(

.Exons()[ea].GetTo() !=

.Exons()[eb].GetTo())

(

.Exons()[ea+1].GetFrom() !=

.Exons()[eb+1].GetFrom())

2*(aright-aleft)+1;

(intersect.

() <= 1)

0;

anum = (

)

.Exons().size()-1;

(; intersect.

() <

.Exons()[anum].GetFrom() ; --anum);

aexon = intersect.

() <=

.Exons()[anum].GetTo();

(!aexon && intersect.

() <

.Exons()[anum+1].GetFrom())

0;

bnum = (

)

.Exons().size()-1;

(; intersect.

() <

.Exons()[bnum].GetFrom(); --bnum);

bexon = intersect.

() <=

.Exons()[bnum].GetTo();

(!bexon && intersect.

() <

.Exons()[bnum+1].GetFrom())

0;

firstcommonpoint = -1;

unique_ptr<CAlignMap> pmapa, pmapb;

(left <= intersect.

())

aright = aexon ?

.Exons()[anum].GetTo() :

.Exons()[anum+1].GetFrom()-1;

bright = bexon ?

.Exons()[bnum].GetTo() :

.Exons()[bnum+1].GetFrom()-1;

(!aexon && bexon)

(

.Exons()[anum].m_ssplice &&

.Exons()[anum+1].m_fsplice)

0;

(left ==

.Exons()[anum].GetTo()+1 &&

.Exons()[anum].m_ssplice)

0;

(right == aright &&

.Exons()[anum+1].m_fsplice)

0;

(aexon && !bexon)

(

.Exons()[bnum].m_ssplice &&

.Exons()[bnum+1].m_fsplice)

0;

(left ==

.Exons()[bnum].GetTo()+1 &&

.Exons()[bnum].m_ssplice)

0;

(right == bright &&

.Exons()[bnum+1].m_fsplice)

0;

(aexon && bexon) {

(firstcommonpoint < 0) {

firstcommonpoint = left;

}

((anum > 0 && left ==

.Exons()[anum].GetFrom() && !

.Exons()[anum].m_fsplice) ||

(bnum > 0 && left ==

.Exons()[bnum].GetFrom() && !

.Exons()[bnum].m_fsplice)) {

pmapa.reset(

(

.Exons(),

.FrameShifts(),

.Strand()));

pmapb.reset(

(

.Exons(),

.FrameShifts(),

.Strand()));

afirst = pmapa->MapOrigToEdited(firstcommonpoint);

bfirst = pmapb->MapOrigToEdited(firstcommonpoint);

(afirst < 0 || bfirst < 0)

0;

(asecond < 0 || bsecond < 0 || (asecond-afirst)%3 != (bsecond-bfirst)%3)

0;

(aexon && aright == right &&

.Exons()[anum].m_ssplice &&

bexon && bright == right &&

.Exons()[bnum].m_ssplice) ++commonspl;

(!aexon && aright == right &&

.Exons()[anum+1].m_fsplice &&

!bexon && bright == right &&

.Exons()[bnum+1].m_fsplice) ++commonspl;

(right == aright)

(right == bright)

firstcommonpoint >= 0 ? commonspl+1 : 0;

(

= 1;

<

.Exons().

(); ++

) {

(!

.Exons()[

-1].m_ssplice || !

.Exons()[

].m_fsplice){

(k->Limits().IntersectingWith(hole)) {

().back().m_ssplice =

;

().front().m_fsplice =

;

(!infront) {

().back().m_ssplice =

;

().front().m_fsplice =

;

(!infront) {

().back().m_ssplice =

;

().back().m_ssplice_sig =

;

().front().m_fsplice =

;

().front().m_fsplice_sig =

;

(

= 0;

<

(exons_with_gaps.size())-1; ++

) {

(exons_with_gaps[

].GetTo() < left_edge && left_edge < exons_with_gaps[

+1].GetFrom()) {

( !exons_with_gaps[

].m_ssplice && !exons_with_gaps[

+1].m_fsplice );

( right_edge >= exons_with_gaps[

+1].GetFrom() );

(

tpos = tlim.

()+del; left_edge < 0 && tpos <= tlim.

(); tpos += 3) {

(exons_with_gaps[

].GetTo() < right_edge && right_edge < exons_with_gaps[

+1].GetFrom()) {

( !exons_with_gaps[

].m_ssplice && !exons_with_gaps[

+1].m_fsplice );

( left_edge <= exons_with_gaps[

].GetTo() );

(

tpos = tlim.

()-del; right_edge < 0 && tpos >= tlim.

(); tpos -= 3) {

(

=0,j=0;

<

.size() || j<

.size(); ) {

(

==

.size())

(j==

.size())

(

[

].GetTo()+1<

[j].GetFrom())

(

[j].GetTo()+1<

[

].GetFrom())

[j].Extend(

[

++]);

(j+1<

.size() &&

[j].GetTo()+1>=

[j+1].GetFrom()) {

[j+1].Extend(

[j]);

().back().m_ident = 0;

(indl->IsDeletion())

TInDels::const_iterator

= indl;

(

()[0].Limits().NotEmpty()) {

().front().AddFrom(-amount);

().back().AddTo(amount);

&

(ios_base& iob)

*&p = iob.pword(m_index);

*c =

*

(p);

iob.register_callback(ios_callback, m_index);

ios_callback(ios_base::event e, ios_base& iob,

index)

(e == ios_base::erase_event) {

*

(iob.pword(index));

}

(e == ios_base::copyfmt_event) {

*&p = iob.pword(index);

*old =

*

(p);

is.setstate(ios::failbit);

.print(os);

os;

* dot =

;

os << (

.empty()?dot:

) <<

;

os << (

.empty()?dot:

) <<

;

os << (

+1) <<

;

os << (

+1) <<

;

(

< 0) os << dot;

os <<

; os <<

;

os <<

<<

;

(!

->second.empty())

os <<

<<

->first <<

<<

->second;

rec.

= NStr::StringToNumeric<int>(v[3])-1;

rec.

= NStr::StringToNumeric<int>(v[4])-1;

rec.

= v[5]==dot?

():NStr::StringToNumeric<double>(v[5]);

rec.

= v[7]==dot?-1:NStr::StringToNumeric<int>(v[7]);

model_id_present =

;

(

==

) {

rec.

= NStr::StringToNumeric<Int8>(

);

model_id_present =

;

}

(

==

) {

rec.

= NStr::StringToNumeric<int>(tt[1])-1;

rec.

= NStr::StringToNumeric<int>(tt[2])-1;

(tt.size() > 3 && tt[3] ==

)

(!model_id_present)

(prev_pos < indel.

())

prev_pos = start;

(indel.

() < start)

(prev_pos < end+1)

vector<string> operations;

((*o)[0] ==

) {

o->erase(o->begin());

}

((*o)[0] ==

) {

o->erase(o->begin());

((*o)[0] ==

) {

}

((*o)[0] ==

) {

indels.back().SetStatus(status);

}

((*o)[0] ==

) {

= (

)o->length()-1;

indels.back().SetStatus(status);

= (

)o->length()-1;

indels.back().SetStatus(status);

((

&

)!=0)

;

(

.GeneID()!=0)

(

.RankInGene()!=0)

(

.TrustedGroup()!=0)

(

.TargetLen() > 0)

(

.Ident() > 0)

(

.Weight() > 1)

(!

.ProteinHit().empty())

(

.GetCdsInfo().ReadingFrame().NotEmpty()) {

tCoords =

;

(protcds.

() && protcds != rf) {

(cds_info.

())

[

] +=

+adj+

;

(

.isNMD(50))

[

] +=

;

(NStr::StringToNumeric<TSignedSeqPos>(start)-1,NStr::StringToNumeric<TSignedSeqPos>(stop)-1);

open_cds =

;

confirmed_start =

;

confirmed_stop =

;

has_start =

;

has_stop =

;

tcoords =

;

vector<string>

;

(*

==

) { confirmed_start =

; has_start =

; }

(*

==

) { open_cds =

; has_start =

; }

(*

==

) has_start =

;

(*

==

) { confirmed_stop =

; has_stop =

; }

(*

==

) has_stop =

;

(*

==

) tcoords =

;

.SetRankInGene(NStr::StringToNumeric<int>(

[

]));

.SetTrustedGroup(NStr::StringToNumeric<int>(

[

]));

target =

+target.substr(4);

target =

+target;

.SetTargetId(*target_id);

vector<string> support;

(vector<string>, s, support) {

core = (*s)[0] ==

;

= NStr::StringToNumeric<Int8>(core ? s->substr(1) : *s);

vector<string> trustedmrna;

(vector<string>, s, trustedmrna) {

vector<string> trustedprot;

(vector<string>, s, trustedprot) {

.SetIdent(NStr::StringToNumeric<double>(

[

]));

.SetWeight(NStr::StringToNumeric<double>(

[

]));

protcds =

.GetAlignMap().MapRangeOrigToEdited(protcds,

);

(has_start, has_stop);

reading_frame.

(reading_frame.

()-3);

(has_start, has_stop);

cds_info.

(start,confirmed_start);

cds_info.

(stop,confirmed_stop);

vector<string> stops;

(vector<string>, s, stops) {

vector<string> parts;

pstop =

.GetAlignMap().MapRangeOrigToEdited(pstop,

);

(parts.size() > 2) {

(parts[2] ==

)

(parts[2] ==

)

(parts[2] ==

)

cds_info.

(pstop, status);

max_cds_limits = tlim;

max_cds_limits =

.GetAlignMap().MapRangeOrigToEdited(max_cds_limits,

);

(max_cds_limits.

() < tlim.

())

.SetCdsInfo(cds_info);

.SetCdsInfo(cds_info);

(

.Strand() ==

)

(

.Strand() ==

)

mrna.

=

;

mrna.

=

.Limits().GetFrom();

mrna.

=

.Limits().GetTo();

mrna.

=

.Score();

vector<SGFFrec> exons,cdss;

exon.

=

;

corrections =

.FrameShifts();

(

= 0;

<

.Exons().

(); ++

) {

exon.

[

] = targetid+target;

(

.Strand() ==

) {

exon.

[

] = fs+

+ss;

exon.

[

] = ss+

+fs;

exons.push_back(exon);

cds_limits =

.GetAlignMap().MapRangeEditedToOrig(tcds,

);

cds.

[

] = targetid+ctarget;

cdss.push_back(cds);

(!

.Continuous()) {

(exons.front().start >= 0) {

rec.

= exons.front().start;

(exons.size() > 1 && exons[1].start >= 0);

rec.

= exons[1].start;

(exons.back().end >= 0) {

rec.

= exons.back().end;

(exons.size() > 1 && exons[exons.size()-2].end >= 0);

rec.

= exons[exons.size()-2].end;

rec.

=

;

e->attributes[

] += suffix;

(

.Strand()==

)

phase = (e->tend - e->tstart+1 - phase)%3;

phase = (3-phase)%3;

e->attributes[

] += suffix;

{

( __x, __y ); }

(

.GetFrom()==

.GetFrom())

.SetFrom(

.GetTo()+1);

(

.GetTo()==

.GetTo())

.SetTo(

.GetFrom()-1);

vector<SGFFrec> recs;

recs.push_back(rec);

}

(is >> rec && rec.

== recs.front().seqid && rec.

==

&& rec.

!=

);

tcoords =

;

vector<CModelExon> exons;

vector<TSignedSeqRange> transcript_exons;

(rec.

==

)

(

->type ==

) {

}

(

->type ==

) {

(

->tstart >= 0 &&

->tstrand ==

) {

(!

->attributes[

].empty()) {

splices =

->attributes[

];

ispl = splices.find(

);

(ispl != string::npos) {

fs = splices.substr(0,2);

(ispl+4 == splices.length())

ss = splices.substr(ispl+2,2);

(!

->attributes[

].empty()) {

eident = NStr::StringToNumeric<double>(

->attributes[

]);

(

->start >= 0 &&

->end >= 0)

exons.push_back(

(

->start,

->end,

,

,fs,ss,eident));

(!

->attributes[

].empty()) {

((

)v.size() == 4);

src.

.

(NStr::StringToNumeric<TSignedSeqPos>(v[1])-1);

src.

.

(NStr::StringToNumeric<TSignedSeqPos>(v[2])-1);

exons.push_back(

(1,-1,

,

,fs,ss,eident,

->attributes[

],src));

transcript_exons.push_back(texon);

(

->attributes[

],

->start,

->end, indels);

(!

->attributes[

].empty())

[

] =

->attributes[

];

}

(

->type ==

) {

(

->strand==

) {

(

->tstart < 0) {

}

(

->type ==

) {

(

= 0;

< (

)exons.size(); ++

) {

(

.Limits().IntersectingWith(e.

())) {

(

> 0 && exons[

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

(indels.begin(),indels.end());

(!transcript_exons.empty())

amap =

(

.Exons(), transcript_exons, indels,

.Orientation(), NStr::StringToNumeric<int>(

[

]));

amap =

(

.Exons(), indels,

.Strand());

.FrameShifts() = indels;

os.setstate(ios::failbit);

is.setstate(ios::failbit);

: m_id( model_id), m_core_align(core)

void remove_if(Container &c, Predicate *__pred)

TSignedSeqPos FShiftedMove(TSignedSeqPos orig_pos, int len) const

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

TSignedSeqPos MapOrigToEdited(TSignedSeqPos orig_pos) 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

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

string TargetAccession() const

void RecalculateAlignMap(int left, int right)

CConstRef< objects::CSeq_id > GetTargetId() const

virtual CAlignMap GetAlignMap() const

void SetTargetId(const objects::CSeq_id &id)

void Cut(TSignedSeqRange hole)

CCDSInfo MapFromEditedToOrig(const CAlignMap &amap) const

bool PStop(bool includeall=true) const

void SetStart(TSignedSeqRange r, bool confirmed=false)

CCDSInfo MapFromOrigToEdited(const CAlignMap &amap) const

TSignedSeqRange MaxCdsLimits() const

void Set5PrimeCdsLimit(TSignedSeqPos p)

void Remap(const CRangeMapper &mapper)

bool IsMappedToGenome() const

void SetScore(double score, bool open=false)

bool m_genomic_coordinates

TSignedSeqRange m_reading_frame_from_proteins

TSignedSeqRange Start() const

bool ConfirmedStart() const

TSignedSeqRange m_reading_frame

void Clip(TSignedSeqRange limits)

void AddPStop(SPStop stp)

TSignedSeqRange Cds() const

void CombineWith(const CCDSInfo &another_cds_info)

TSignedSeqRange ReadingFrame() const

TSignedSeqRange m_max_cds_limits

TSignedSeqRange ProtReadingFrame() const

void SetStop(TSignedSeqRange r, bool confirmed=false)

const TPStops & PStops() const

bool ConfirmedStop() const

void Clear5PrimeCdsLimit()

void SetReadingFrame(TSignedSeqRange r, bool protein=false)

bool operator==(const CCDSInfo &another) const

TSignedSeqRange Stop() const

void AddExon(TSignedSeqRange exon, const string &fs="", const string &ss="", double ident=0, const string &seq="", const CInDelInfo::SSource &src=CInDelInfo::SSource())

TSignedSeqPos FShiftedMove(TSignedSeqPos pos, int len) const

void ExtendRight(int amount)

void RemoveExtraFShifts(int left, int right)

bool isNMD(int limit=50) const

void TrimEdgesToFrameInOtherAlignGaps(const TExons &exons_with_gaps)

void AddNormalExon(TSignedSeqRange exon, const string &fs, const string &ss, double ident, bool infront)

virtual void CutExons(TSignedSeqRange hole)

int MutualExtension(const CGeneModel &a) const

TSignedSeqRange TranscriptLimits() const

void Extend(const CGeneModel &a, bool ensure_cds_invariant=true)

EStrand Orientation() const

int FShiftedLen(TSignedSeqRange ab, bool withextras=true) const

const TExons & Exons() const

TSignedSeqRange ReadingFrame() const

virtual CAlignMap GetAlignMap() const

TSignedSeqRange RealCdsLimits() const

TSignedSeqRange TranscriptExon(int i) const

void ReverseComplementModel()

void CombineCdsInfo(const CGeneModel &a, bool ensure_cds_invariant=true)

void SetStrand(EStrand s)

void RemoveShortHolesAndRescore(const CGnomonEngine &gnomon)

virtual void Clip(TSignedSeqRange limits, EClipMode mode, bool ensure_cds_invariant=true)

void SetCdsInfo(const CCDSInfo &cds_info)

void AddGgapExon(double ident, const string &seq, const CInDelInfo::SSource &src, bool infront)

TSignedSeqRange Limits() const

bool IsSubAlignOf(const CGeneModel &a) const

int HasCompatibleOverlap(const CGeneModel &a, int min_overlap=2) const

const CCDSInfo & GetCdsInfo() const

vector< CModelExon > TExons

bool CdsInvariant(bool check_start_stop=true) const

TSignedSeqRange MaxCdsLimits() const

bool ConfirmedStart() const

void ExtendLeft(int amount)

TInDels GetInDels(bool fs_only) const

static string TypeToString(int type)

void Remap(const CRangeMapper &mapper)

int isCompatible(const CGeneModel &a) const

void GetScore(CGeneModel &model, bool extend5p=false, bool obeystart=false, bool extend_max_cds=false) const

int GetMinIntronLen() const

static CRef< CSeq_id > GnomonMRNA(Int8 id)

static CRef< CSeq_id > ToSeq_id(const string &str)

static string ToString(const CSeq_id &id)

TSignedSeqPos Loc() const

EStatus GetStatus() const

CInDelInfo::SSource m_source

TSignedSeqPos GetFrom() const

const TSignedSeqRange & Limits() const

TSignedSeqPos GetTo() const

void Extend(const CModelExon &e)

map< IOS_BASE *, T > TMap

CStreamState(const T &deflt)

bool operator==(const CSupportInfo &s) const

CSupportInfo(Int8 model_id, bool core=false)

bool operator<(const CSupportInfo &s) const

container_type::iterator iterator

const_iterator begin() const

const_iterator end() const

iterator_bool insert(const value_type &val)

const_iterator find(const key_type &key) const

iterator_bool insert(const value_type &val)

parent_type::iterator iterator

const_iterator end() const

const_iterator lower_bound(const key_type &key) const

bool Empty(const CNcbiOstrstream &src)

static DLIST_TYPE *DLIST_NAME() next(DLIST_LIST_TYPE *list, DLIST_TYPE *item)

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

static const struct attribute attributes[]

static const TDS_WORD limits[]

CNcbiIstream & Getline(CNcbiIstream &is, string &line)

CStreamState< string > contig_stream_state(kEmptyStr)

CNcbiOstream & printGFF3(CNcbiOstream &os, CAlignModel a)

TSignedSeqRange StringToRange(const string &s)

void readGFF3Gap(const string &gap, TSignedSeqPos start, TSignedSeqPos end, TInDels &indels)

void ParseAttributes(map< string, string > &attributes, CAlignModel &a)

CNcbiOstream & operator<<(CNcbiOstream &s, const setcontig &c)

CStreamState< EModelFileFormat > model_file_format_state(eGFF3FileFormat)

CNcbiIstream & InputError(CNcbiIstream &is)

CStreamState< pair< string, string > > line_buffer(make_pair(kEmptyStr, kEmptyStr))

void CollectAttributes(const CAlignModel &a, map< string, string > &attributes)

TSignedSeqRange operator-(TSignedSeqRange a, TSignedSeqRange b)

void Ungetline(CNcbiIstream &is)

CNcbiIstream & operator>>(CNcbiIstream &is, const getcontig &c)

pair< int, int > ExonNumsForInterval(const CGeneModel &a, TSignedSeqRange &intersect)

string BuildGFF3Gap(int &prev_pos, const CInDelInfo &indel)

CNcbiIstream & readGFF3(CNcbiIstream &is, CAlignModel &align)

bool Precede(TSignedSeqRange l, TSignedSeqRange r)

bool Include(TSignedSeqRange big, TSignedSeqRange small)

void ReverseComplement(const BidirectionalIterator &first, const BidirectionalIterator &last)

vector< CInDelInfo > TInDels

#define ITERATE(Type, Var, Cont)

ITERATE macro to sequence through container elements.

#define ERASE_ITERATE(Type, Var, Cont)

Non-constant version with ability to erase current element, if container permits.

int TSignedSeqPos

Type for signed sequence position.

#define VECTOR_ERASE(Var, Cont)

Use this macro inside body of ERASE_ITERATE cycle to erase from vector-like container.

#define NON_CONST_ITERATE(Type, Var, Cont)

Non constant version of ITERATE macro.

void swap(NCBI_NS_NCBI::pair_base_member< T1, T2 > &pair1, NCBI_NS_NCBI::pair_base_member< T1, T2 > &pair2)

#define ERR_POST(message)

Error posting with file, line number information but without error codes.

void Error(CExceptionArgs_Base &args)

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

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

int64_t Int8

8-byte (64-bit) signed integer

position_type GetLength(void) const

bool NotEmpty(void) const

bool IntersectingWith(const TThisType &r) const

TThisType & CombineWith(const TThisType &r)

static TThisType GetEmpty(void)

static position_type GetWholeFrom(void)

CRange< TSignedSeqPos > TSignedSeqRange

static TThisType GetWhole(void)

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.

CNcbiIstream & NcbiGetlineEOL(CNcbiIstream &is, string &str, string::size_type *count=NULL)

Read from "is" to "str" the next line (taking into account platform specifics of End-of-Line)

IO_PREFIX::ostream CNcbiOstream

Portable alias for ostream.

IO_PREFIX::istream CNcbiIstream

Portable alias for istream.

static string DoubleToString(double value, int precision=-1, TNumToStringFlags flags=0)

Convert double to string.

static list< string > & Split(const CTempString str, const CTempString delim, list< string > &arr, TSplitFlags flags=0, vector< SIZE_TYPE > *token_pos=NULL)

Split a string using specified delimiters.

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 StartsWith(const CTempString str, const CTempString start, ECase use_case=eCase)

Check if a string starts with a specified prefix value.

static bool SplitInTwo(const CTempString str, const CTempString delim, string &str1, string &str2, TSplitFlags flags=0)

Split a string into two pieces using the specified delimiters.

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.

@ fConvErr_NoThrow

Do not throw an exception on error.

@ fAllowLeadingSymbols

Ignore leading non-numeric characters.

@ fSplit_MergeDelimiters

Merge adjacent delimiters.

#define NCBI_XALGOGNOMON_EXPORT

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.

unsigned int

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

constexpr auto sort(_Init &&init)

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

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

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

const struct ncbi::grid::netcache::search::fields::KEY key

const GenericPointer< typename T::ValueType > T2 value

Useful/utility classes and methods.

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

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

bool operator()(const TSignedSeqRange &__x, const TSignedSeqRange &__y) const

void print(CNcbiOstream &os) const

map< string, string > attributes

int g(Seg_Gsm *spe, Seq_Mtf *psm, Thd_Gsm *tdg)

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