Home - News ( United States | United Kingdom | Italy | Germany ) - Football scores

Showing content from http://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/doxyhtml/score_8cpp_source.html below:

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

ii = (strand ==

) ?

: SeqLen()-1-

;

(ii < 0 || ii+2 >= SeqLen())

;

(ss[ii] !=

|| ss[ii+1] !=

|| ss[ii+2] !=

)

;

(ii < 0 || ii+2 >=

())

;

((ss[ii] !=

|| ss[ii+1] !=

|| ss[ii+2] !=

) &&

(ss[ii] !=

|| ss[ii+1] !=

|| ss[ii+2] !=

) &&

(ss[ii] !=

|| ss[ii+1] !=

|| ss[ii+2] !=

))

;

(strand ==

) {

(strand ==

) {

(ii-1 < 0 || ii >=

())

;

(ss[ii-1] !=

|| ss[ii] !=

)

;

(ii < 0 || ii+1 >=

())

;

(ss[ii] !=

|| ss[ii+1] !=

)

;

&ss.front()+ii;

(

>

)

0;

score =

[strand][frame][

];

(

> 0) score -=

[strand][frame][

-1];

(strand == 0 || strand == 1);

x =

.ReadingFrame().NotEmpty() ?

.ReadingFrame().GetFrom() :

.Limits().GetFrom();

y =

.ReadingFrame().NotEmpty() ?

.ReadingFrame().GetFrom() :

.Limits().GetFrom();

.ID()<

.ID();

.ID()==

;

(

.MaxCdsLimits().Empty() ?

.Limits().GetFrom() :

.MaxCdsLimits().GetFrom() );

: m_acceptor(

), m_donor(d), m_start(stt), m_stop(stp), m_cdr(cr), m_ncdr(ncr), m_intrg(ing),

m_align_list(cls), m_fshifts(initial_fshifts), m_map(from,to), m_chunk_start(from), m_chunk_stop(to), m_mpp(mpp)

(

= 1;

< align.

().

(); ++

) {

(!align.

()[

-1].m_ssplice || !align.

()[

].m_fsplice) {

hole_len = align.

()[

].GetFrom()-align.

()[

-1].GetTo()-1;

(hole_len <= intron_params.

()) {

(hole_len%3 != 0) {

p = (p+align.

()[

].GetFrom())/2;

(

strand = 0; strand < 2; ++strand) {

(

frame = 0; frame < 3; ++frame) {

(

ph = 0; ph < 2; ++ph) {

}

(bad_alloc&) {

left = ig->first;

right = ig->first+ig->second-1;

(

pnt = left; pnt <= right; ++pnt) {

(

jj = ig->first; jj <= ig->

+ (

)ig->second->GetInDelV().length() - 1; ++jj) {

RepeatMargin = 25;

(

rpta = 0; rpta <

; ) {

(rpta <

&&

(sequence[rpta]))

(rptb+1 <

&&

(sequence[rptb+1]))

(rptb-rpta+1 > 2*RepeatMargin) {

repeats[

].insert(

);

c = sequence[

];

NLimit = 6;

opposite =

;

(it == jt)

;

align.

(mapper);

(strand ==

)

(extraNs5p,extraNs3p);

mRNA.insert(mRNA.begin(),extraNs5p,

);

mRNA.insert(mRNA.end(),extraNs3p,

);

(

k = extraNs5p; k < (

)mRNA.size()-extraNs3p; ++k) {

(strand ==

) {

(

pnt =

; pnt <=

; ++pnt) {

(

pnt =

; pnt <=

; ++pnt) {

(

pnt =

; pnt <=

; ++pnt) {

(

pnt =

; pnt <=

; ++pnt) {

allaligns.

(align);

repeats[strand].erase(

);

ff = (strand ==

) ? 2-right%3 : right%3;

(

frame = 0; frame < 3; ++frame) {

(!e->m_ssplice && right < align.

().

()) {

ff = (strand ==

) ? 2-right%3 : right%3;

(

frame = 0; frame < 3; ++frame) {

RepeatFreeMargin = 75;

(

=

(0,

.GetFrom()-RepeatFreeMargin);

<

.GetFrom(); ++

)

repeats[align.

()].erase(

);

repeats[align.

()].erase(

);

(

strand = 0; strand < 2; ++strand) {

(

: repeats[strand]) {

strand = algn.

();

(

k = 1; k < algn.

().size(); ++k)

(algn.

()[k-1].m_ssplice)

= algn.

()[k-1].GetTo();

(algn.

()[k].m_fsplice)

= algn.

()[k].GetFrom();

[strand][

-1] = 0;

(

k = 1; k < algn.

().size(); ++k)

introna = algn.

()[k-1].GetTo()+1;

intronb = algn.

()[k].GetFrom()-1;

(algn.

()[k-1].m_ssplice)

(algn.

()[k].m_fsplice)

(algn.

()[k-1].m_ssplice && algn.

()[k].m_fsplice)

(

pnt = introna; pnt <= intronb; ++pnt)

(

k = 0; k < algn.

().size(); ++k)

exona = algn.

()[k].GetFrom();

exonb = algn.

()[k].GetTo();

(

pnt = exona; pnt <= exonb; ++pnt)

(strand ==

)

+= 3;

(

strand = 0; strand < 2; ++strand)

(

frame = 0; frame < 3; ++frame)

(

strand = 0; strand < 2; ++strand)

(strand ==

)

strand = algn.

();

(cds_lim.

())

;

(strand ==

)

(

k = 0; k < algn.

().

(); ++k) {

(

k = 0; k < algn.

().

(); ++k) {

(

strand = 0; strand < 2; ++strand)

(strand ==

)

lstp =

(

(

)+1,lstp);

lstp =

(

(

)-2,lstp);

(

strand = 0; strand < 2; ++strand)

(score ==

()) score = 0;

(score ==

()) score = 0;

(pcsf_slice !=

) {

& score = (*pcsf_slice->

)[strand];

(pcsf_slice->

!=

)

(codon_left < 0 || codon_left >

-3)

frame = strand ==

? (3-codon_left%3)%3 : (2+codon_left%3)%3;

(pcsf_score > 0) {

(

step = 0; step < 3; ++step)

[strand][frame][codon_left+step] = pcsf_score;

(

frame = 0; frame < 3; ++frame)

(strand ==

)

codonshift = (frame+

)%3;

codonshift = (frame-(

)

)%3;

(codonshift < 0) codonshift += 3;

score =

.

(s,ii,codonshift);

(score ==

()) score = 0;

lstp[

] =

(lstp[

-1],lstp[

]);

(

strand = 0; strand < 2; ++strand)

(

frame = 0; frame < 3; ++frame)

left =

+1-(strand==

?

.Left():

.Right());

right =

+(strand==

?

.Right():

.Left());

right =

(

-1,right);

left =

+1-(strand==

?

.Left():

.Right());

right =

+(strand==

?

.Right():

.Left());

right =

(

-1,right);

left =

+1-(strand==

?

.Left():

.Right());

right =

+(strand==

?

.Right():

.Left());

right =

(

-1,right);

left =

+1-(strand==

?

.Left():

.Right());

right =

+(strand==

?

.Right():

.Left());

left =

(0,left);

right =

(

-1,right);

strand = algn.

();

(algn.

().front().m_fsplice_sig ==

|| algn.

().front().m_ssplice_sig ==

) {

[strand][p] = consensuspenalty;

[strand][p] = consensuspenalty;

(algn.

().back().m_fsplice_sig ==

|| algn.

().back().m_ssplice_sig ==

) {

[strand][p] = consensuspenalty;

[strand][p] = consensuspenalty;

NonConsensusMargin = 50;

(consensuspenalty !=

())

strand = algn.

();

(

k = 1; k < algn.

().

(); ++k)

(algn.

()[k-1].m_ssplice && algn.

()[k].m_fsplice)

;

= algn.

()[k-1].GetTo();

= algn.

()[k].GetFrom();

(i <= a+NonConsensusMargin || i >=

-NonConsensusMargin)

[strand][

] = consensuspenalty;

[strand][

] = consensuspenalty;

(strand ==

)

(!algn.

() && algn.

().front().m_ssplice_sig !=

)

=

(2,lim.

()-NonConsensusMargin);

[strand][

] = consensuspenalty;

[strand][

] = consensuspenalty;

[strand][

] = consensuspenalty;

(!algn.

() && algn.

().back().m_fsplice_sig !=

)

=

(

-4,lim.

()+NonConsensusMargin);

[strand][

] = consensuspenalty;

[strand][

] = consensuspenalty;

[strand][

] = consensuspenalty;

(!algn.

() && algn.

().back().m_fsplice_sig !=

)

=

(

-4,lim.

()+NonConsensusMargin);

[strand][

] = consensuspenalty;

[strand][

] = consensuspenalty;

[strand][

] = consensuspenalty;

(!algn.

() && algn.

().front().m_ssplice_sig !=

)

=

(2,lim.

()-NonConsensusMargin);

[strand][

] = consensuspenalty;

[strand][

] = consensuspenalty;

[strand][

] = consensuspenalty;

stpT = 1, stpTA = 2, stpTG = 4;

(

strand = 0; strand < 2; ++strand)

(strand ==

) {

(s[

+1] ==

)

[strand][1][

] |= stpTA|stpTG;

ii =

-2-

;

(s[ii+1] ==

&& s[ii+2] ==

)

[strand][0][

] |= stpT;

(s[ii+1] ==

&& s[ii+2] ==

)

[strand][0][

] |= stpT;

(s[ii+1] ==

&& s[ii+2] ==

)

[strand][0][

] |= stpT;

(s[ii+1] ==

)

[strand][1][

] |= stpTA|stpTG;

(s[ii+1] ==

)

[strand][1][

] |= stpTA;

(s[ii-1] ==

&& s[ii] ==

)

[strand][1][

] |= stpTA;

(s[ii-1] ==

&& s[ii] ==

)

[strand][1][

] |= stpTG;

strand = algn.

();

(cds_lim.

())

;

(strand ==

)

(

k = 0; k < algn.

().

()-1; ++k)

(algn.

()[k].m_ssplice && algn.

()[k+1].m_fsplice &&

>= cds_lim.

() &&

<= cds_lim.

())

(

k = 1; k < algn.

().

(); ++k)

(

> 0 && algn.

()[k-1].m_ssplice && algn.

()[k].m_fsplice &&

>= cds_lim.

() &&

<= cds_lim.

())

(strand ==

) {

(

k =

-donor.

()+1; k <=

+donor.

(); ++k) {

= contig_len-1-

;

(strand ==

) {

(

k =

-acceptor.

()+1; k <=

+acceptor.

(); ++k) {

= contig_len-2-

;

codonshift = (

+3-frame)%3;

codonshift = (2-codonshift)%3;

scr = cdr.

(ds[strand], pos, codonshift);

s = ncdr.

(ds[strand], pos);

vector<CModelExon>& exons = model.

();

num_exons = (

)model.

().size();

splicescr(mrna.size(),0);

(strand ==

) {

(

= 1;

< num_exons; ++

) {

shift += mrnamap.

(exons[

-1].GetFrom(),exons[

-1].GetTo());

(exons[

-1].m_ssplice && exons[

-1].m_ssplice_sig !=

) {

= exons[

-1].GetTo();

(

k =

-donor.

()+1; k <=

+donor.

(); ++k) {

splicescr[shift] = scr;

(exons[

].m_fsplice && exons[

].m_fsplice_sig !=

) {

= exons[

].GetFrom()-1;

(

k =

-acceptor.

()+1; k <=

+acceptor.

(); ++k) {

splicescr[shift] += scr;

shift = (

)mrna.size()-1;

(

= 1;

< num_exons; ++

) {

shift -= mrnamap.

(exons[

-1].GetFrom(),exons[

-1].GetTo());

(exons[

-1].m_ssplice && exons[

-1].m_ssplice_sig !=

) {

= contig_len-2-exons[

-1].GetTo();

(

k =

-acceptor.

()+1; k <=

+acceptor.

(); ++k) {

splicescr[shift] = scr;

(exons[

].m_fsplice && exons[

].m_fsplice_sig !=

) {

= contig_len-1-exons[

].GetFrom();

(

k =

-donor.

()+1; k <=

+donor.

(); ++k) {

splicescr[shift] += scr;

(

frame = 0; frame < 3; ++frame) {

(frame==best_frame || best_frame==-1)

cdrscr[frame].resize(mrna.size(), 0);

(pcsf_slice !=

) {

(

frame = 0; frame < 3; ++frame) {

(frame==best_frame || best_frame==-1) {

(

codon_left = frame; codon_left <= (

)mrna.size()-3; codon_left += 3) {

(pcsf_score > 0) {

(

step = 0; step < 3; ++step)

cdrscr[frame][codon_left+step] = pcsf_score;

(

frame = 0; frame < 3; ++frame) {

(frame==best_frame || best_frame==-1) {

(

= 0;

< (

)mrna.size(); ++

) {

codonshift = (

-frame)%3;

scr = cdr.

(mrna,

,codonshift);

s = ncdr.

(mrna,

);

cdrscr[frame][

] += scr+splicescr[

];

cdrscr[frame][

] += cdrscr[frame][

-1];

best_frame_initial = best_frame;

(

frame = 0; frame < 3; ++frame) {

(frame==best_frame_initial || best_frame_initial==-1) {

(

= 0;

< (

)stops[frame].

();

++) {

stop = stops[frame][

];

prev_stop = stops[frame][

-1];

TIVec::iterator it_a = lower_bound(starts[frame].begin(),starts[frame].end(),prev_stop+3);

(it_a == starts[frame].end() || *it_a >= stop)

TIVec::iterator it_b = it_a+1;

(*it_a < 0 && it_b != starts[frame].end() && *it_b < stop)

( ; it_b != starts[frame].end() && *it_b < stop; ++it_b);

(TIVec::iterator it = it_a; it != it_b; it++) {

(stop-start-(start>=0?0:3) < 30)

s = cdrscr[frame][stop-1]-cdrscr[frame][start+2+(start>=0?0:3)];

(start >= stt.

()+2) {

stt_score = stt.

(mrna,pnt);

(

k = pnt-stt.

()+1; k <= pnt+stt.

(); ++k) {

sn = ncdr.

(mrna,k);

(strand ==

) pnt = contig_len-1-pnt;

stt_score = stt.

(ds[strand],pnt);

(

k = pnt-stt.

()+1; k <= pnt+stt.

(); ++k) {

sn = ncdr.

(ds[strand],k);

stp_score = stp.

(mrna,stop-1);

(

k = stop-stp.

(); k < stop+stp.

(); ++k) {

sn = ncdr.

(mrna,k);

(s >= best_score) {

best_score +=

(1.,0.3*best_score);

starts[3], stops[3];

(

fr = 0; fr < 3; ++fr) {

CCDSInfo::TPStops::iterator it = find(pstops.begin(), pstops.end(), pstop);

(it != pstops.end())

mrna_len = (

)mrna.size();

(

fr = 0; fr < 3; ++fr) {

first_stop = stops[fr][0];

(first_stop >= 3) {

(first_stop < mrna_len-2) {

first_start = -1;

(!starts[fr].

()) {

first_start = starts[fr][0];

(first_start < 0 && starts[fr].

() > 1)

first_start = starts[fr][1];

(first_start >= 0 && first_start <= first_stop-6) {

fivep_rf = first_start+3;

(stt.

() || stops[fr][0] >= 0) {

threep_rf = first_stop-1;

(stops[fr][0] < 0) {

(first_stop < mrna_len-2) {

last_stop = stops[fr][(

)stops[fr].

()-1];

(last_stop >= mrna_len-2)

last_stop = stops[fr][(

)stops[fr].

()-2];

(start > last_stop && start <= mrna_len-6) {

fivep_rf = start+3;

threep_rf = mrna_len-(mrna_len-fr)%3-1;

best_start, best_stop;

best_score =

(model, mrna, mrnamap, starts, stops, frame, best_start, best_stop, extend5p);

is_open =

;

(best_start == 0) {

}

(best_start<0 && starts[frame].

() > 1) {

new_start = starts[frame][1];

newlen = best_stop-new_start;

oldlen = best_stop-best_start;

best_start = new_start;

(cds_info.

() && best_start != starts[frame].back()) {

has_start = best_start>=0;

(

(best_reading_frame, cds_info.

()))

upstream_stop = frame-3;

first_start = best_start;

((

)mrna.size() - best_stop >=3)

(

= upstream_stop+3;

< best_stop;

+= 3) {

CCDSInfo::TPStops::iterator it = find(pstops.begin(), pstops.end(), pstop);

(it != pstops.end())

status = it->m_status;

cds_info.

(pstop, status);

cds_info.

(best_score, is_open);

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

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

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

CCDSInfo MapFromEditedToOrig(const CAlignMap &amap) const

void SetStart(TSignedSeqRange r, bool confirmed=false)

CCDSInfo MapFromOrigToEdited(const CAlignMap &amap) const

TSignedSeqRange MaxCdsLimits() const

void Set5PrimeCdsLimit(TSignedSeqPos p)

bool IsMappedToGenome() const

void SetScore(double score, bool open=false)

TSignedSeqRange Start() const

bool ConfirmedStart() const

void AddPStop(SPStop stp)

TSignedSeqRange ReadingFrame() const

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)

TSignedSeqRange Stop() const

virtual double Score(const CEResidueVec &seq, int i, int codonshift) const =0

void ExtendRight(int amount)

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

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

const TExons & Exons() const

vector< CCDSInfo > * SetEdgeReadingFrames()

TSignedSeqRange ReadingFrame() const

virtual CAlignMap GetAlignMap() const

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

void SetCdsInfo(const CCDSInfo &cds_info)

TSignedSeqRange Limits() const

void AddComment(const string &comment)

const CCDSInfo & GetCdsInfo() const

vector< CModelExon > TExons

TSignedSeqRange MaxCdsLimits() const

bool ConfirmedStart() const

void ExtendLeft(int amount)

void Remap(const CRangeMapper &mapper)

double SelectBestReadingFrame(const CGeneModel &model, const CEResidueVec &mrna, const CAlignMap &mrnamap, TIVec starts[3], TIVec stops[3], int &frame, int &best_start, int &best_stop, bool extend5p=true) const

double DonorScore(int l, EStrand strand) const

unique_ptr< SGnomonEngineImplData > m_data

double PointCodingScore(int l, EStrand strand, int frame) const

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

double AcceptorScore(int l, EStrand strand) const

virtual double Score(const CEResidueVec &seq, int i) const =0

bool isReadingFrameRightEnd(int i, int strand) const

bool OpenCodingRegion(int a, int b, int strand, int frame) const

void Init(CResidueVec &original_sequence, bool leftwall, bool rightwall, double consensuspenalty, const CGnomonAnnotator_Base::TIntMap &notbridgeable_gaps_len, const CGnomonAnnotator_Base::TGgapInfo &ggapinfo, SPhyloCSFSlice *pcsf_slice=nullptr)

bool isStop(int i, int strand) const

bool isConsensusIntron(int i, int j, int strand) const

TSignedSeqPos From() const

const CNonCodingRegion & m_intrg

bool OpenIntergenicRegion(int a, int b) const

TSignedSeqPos m_chunk_stop

const CTerminal & m_donor

bool isAG(int i, int strand) const

const CTerminal & m_start

double IntergenicScore(int a, int b, int strand) const

const CNonCodingRegion & m_ncdr

bool isGT(int i, int strand) const

const EResidue * SeqPtr(int i, int strand) const

TGeneModelList m_align_list

double CodingScore(int a, int b, int strand, int frame) const

bool isReadingFrameLeftEnd(int i, int strand) const

bool isStart(int i, int strand) const

TSignedSeqPos m_chunk_start

double NonCodingScore(int a, int b, int strand) const

const CCodingRegion & m_cdr

CResidueVec ConstructSequenceAndMaps(const TGeneModelList &aligns, const CResidueVec &original_sequence)

bool OpenNonCodingRegion(int a, int b, int strand) const

const CTerminal & m_acceptor

bool StopInside(int a, int b, int strand, int frame) const

CSeqScores(const CTerminal &a, const CTerminal &d, const CTerminal &stt, const CTerminal &stp, const CCodingRegion &cr, const CNonCodingRegion &ncr, const CNonCodingRegion &ing, const CIntronParameters &intron_params, TSignedSeqPos from, TSignedSeqPos to, const TGeneModelList &cls, const TInDels &initial_fshifts, double mpp, const CGnomonEngine &gnomon)

virtual double Score(const CEResidueVec &seq, int i) const =0

iterator_bool insert(const value_type &val)

const_iterator begin() const

parent_type::iterator iterator

const_iterator end() const

static DLIST_TYPE *DLIST_NAME() first(DLIST_LIST_TYPE *list)

static const TDS_WORD limits[]

vector< TResidue > CResidueVec

bool Include(TSignedSeqRange big, TSignedSeqRange small)

const EResidue k_toMinus[5]

list< CGeneModel > TGeneModelList

bool IsStopCodon(const Res *seq, int strand=ePlus)

vector< CInDelInfo > TInDels

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

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

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)

EResidue fromACGT(TResidue c)

#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 NCBI_THROW(exception_class, err_code, message)

Generic macro to throw an exception, given the exception class, error code and message string.

int64_t Int8

8-byte (64-bit) signed integer

position_type GetLength(void) const

bool NotEmpty(void) const

bool IntersectingWith(const TThisType &r) 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)

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

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

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

set< CGeneModel, SAlignOrder > TAlignSet

static bool s_AlignLeftLimitOrder(const CGeneModel &ap, const CGeneModel &bp)

TSignedSeqPos AlignLeftLimit(const CGeneModel &a)

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

TSignedSeqRange operator()(TSignedSeqRange r, bool withextras=true) const

const CAlignMap & m_seq_map

CIndelMapper(const CAlignMap &seq_map)

bool operator()(const CGeneModel &a)

bool operator()(const CGeneModel &a, const CGeneModel &b) const

TSignedSeqRange CompactRange(int s, TSignedSeqRange edited_range) const

TPhyloCSFScore Score(int s, TSignedSeqPos codon_left) const

const array< SPhyloCSFCompactScore, 2 > * m_scoresp

RetroSearch is an open source project built by @garambo | Open a GitHub Issue

Search and Browse the WWW like it's 1997 | Search results from DuckDuckGo

HTML: 3.2 | Encoding: UTF-8 | Version: 0.7.4