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

= (

-1)/m_step;

delx =

((

+1)*m_step,MaxLen())-

;

dely = (

== 0 ? 1 : m_clscore[

-1])-m_clscore[

];

(dely/m_step*delx+m_clscore[

]);

: m_stop(point), m_strand(strn),

m_score(

()), m_leftstate(0), m_terminal(0),

:

(strn,point,seqscr), m_phase(ph),

m_prevexon(0), m_mscore(

()),

m_param(&exon_params)

(frame < 0) frame += 3;

(frame < 0) frame += 3;

(frame < 0) frame += 3;

:

(strn,point,2,seqscr,exon_params)

:

(strn,point,ph,seqscr,exon_params)

((ph+1)%3 ==

.Phase())

0;

:

(strn,point,ph,seqscr,exon_params)

ph0 = (ph1-

)%3;

(ph0 < 0) ph0 += 3;

ph1 = (ph0+

)%3;

:

(strn,point,ph,seqscr,exon_params)

:

(strn,point,seqscr), m_phase(ph),

m_param(&intron_params)

shift =

.Stop()-

.Start();

m_param(&intergenic_params)

CMarkov_chain_params::TProbabilities::const_iterator

= from.

().begin();

m_score[

] = (*

++)->GetValue();

m_score[

] = (*

++)->GetValue();

m_score[

] = (*

++)->GetValue();

m_score[

] = (*

++)->GetValue();

m_score[

] = 0.25*(m_score[

]+m_score[

]+m_score[

]+m_score[

]);

m_score[

] = 0.25*(m_score[

]+m_score[

]+m_score[

]+m_score[

]);

(first < 0 || last >= (

)seq.size())

();

((seq[

+1] !=

|| seq[

+2] !=

|| seq[

+3] !=

) &&

(seq[

+1] !=

|| seq[

+2] !=

|| seq[

+3] !=

) &&

(

= 0;

< num; ++

)

[

] /= sum;

(

= num-2;

>= 0; --

)

(

= 0;

< num; ++

)

(seqlen >=

()) {

through = (l2-2*seqlen)*w/2*exp(

[ifirst]);

ilast = (seqlen-1)/

;

(

= 0;

< ilast; ++

) {

w = seqlen-ilast*

;

l2 = ilast*

+1+seqlen;

through += (l2-2*seqlen)*w/2*exp(

[ilast]);

through = (

()-seqlen-through)/

();

through = (through <= 0) ?

() :

(through);

(

+

);

(

= 0;

< 3; ++

) {

(

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

(

+

);

(

= 0;

< 3; ++

)

(vector<CInputModel*>,

, all_created_models)

all_created_models.clear();

(

->second.empty())

->second.push_back(make_pair<int,CInputModel*>(101,

));

TCGContentList::iterator

= list.begin();

(

->first <= low ) {

= list.insert(

, *

);

(high < i->

) {

= list.insert(

, *

);

}

(high >

->first) {

->second = input_model;

<

CParam>

((*p)->GetParam().Which() != choice)

low = (*p)->GetGc_content_range().GetFrom();

high = (*p)->GetGc_content_range().GetTo();

(!( 0<=low && low < high && high <= 100) )

(input_model==

)

all_created_models.push_back(input_model);

StoreParam(CParam::class_id(), input_model, low, high);

DeleteAllCreatedModels();

(cgcontent >= 100)

(i_param == params.end())

(cgcontent < i->

) {

(

->second ==

) {

*params.begin()->second.front().second;

double m_internalphase[3][3]

CExonParameters(const objects::CGnomon_param::C_Param &from)

void UpdatePrevExon(const CExon &e)

const CExonParameters * m_param

CExon(EStrand strn, int point, int ph, const CSeqScores &seqscr, const CExonParameters &params)

double BranchScore(const CHMM_State &) const

CFirstExon(EStrand strn, int ph, int point, const CSeqScores &seqscr, const CExonParameters &params)

double LengthScore() const

void DeleteAllCreatedModels()

void ReadParameters(const objects::CGnomon_params &hmm_params_asn, objects::CGnomon_param::C_Param::E_Choice choice)

vector< pair< int, CInputModel * > > TCGContentList

TCGContentList & GetCGList(const string &type)

void StoreParam(const string &type, CInputModel *input_model, int low, int high)

SDetails(const objects::CGnomon_params &hmm_params_asn)

const CInputModel & GetParameter(const string &type, int cgcontent) const

CHMMParameters(const objects::CGnomon_params &hmm_params_asn)

CRef< SDetails > m_details

const CInputModel & GetParameter(const string &type, int cgcontent) const

const CSeqScores * m_seqscr

const CTerminal * m_terminal

CHMM_State(EStrand strn, int point, const CSeqScores &seqscr)

const CHMM_State * m_leftstate

static void Error(const string &label)

void SetSeqLen(int seqlen) const

CIntergenicParameters(const objects::CGnomon_param::C_Param &from)

CIntergenic(EStrand strn, int point, const CSeqScores &seqscr, const CIntergenicParameters &params)

double BranchScore(const CHMM_State &) const

const CIntergenicParameters * m_param

double LengthScore() const

CInternalExon(EStrand strn, int ph, int point, const CSeqScores &seqscr, const CExonParameters &params)

void SetSeqLen(int seqlen) const

CIntronParameters(const objects::CGnomon_param::C_Param &from)

const CIntronParameters * m_param

double BranchScore(const CHMM_State &) const

CIntron(int j_in, char amin_in, char don11, char don21, char acs11, char acs21, const CAlignInfo &prev, const CAlignInfo &cur, const CNSeq &nseq_in, const CProSplignScaledScoring &scoring)

double ClosingLengthScore() const

double LengthScore() const

CLastExon(EStrand strn, int ph, int point, const CSeqScores &seqscr, const CExonParameters &params)

double BranchScore(const CHMM_State &) const

CLength_distribution_params –.

double Score(int l) const

void Init(const objects::CLength_distribution_params &from)

double Through(int seqlen) const

double ClosingScore(int l) const

void InitScore(int l, const objects::CMarkov_chain_array &from)

double Score(const EResidue *seq) const

void Init(const objects::CMarkov_chain_params &hmm_param_asn)

void InitScore(const objects::CMarkov_chain_params &hmm_param_asn)

void Average(Type &mc0, Type &mc1, Type &mc2, Type &mc3)

CMarkov_chain_params –.

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

const CTerminal & Acceptor() const

const CTerminal & Stop() const

double StartScore(int i, int strand) const

bool OpenIntergenicRegion(int a, int b) const

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

const CTerminal & Start() const

double AcceptorScore(int i, int strand) const

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

double DonorScore(int i, int strand) const

const CTerminal & Donor() const

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

double StopScore(int i, int strand) const

double BranchScore(const CHMM_State &) const

double LengthScore() const

CSingleExon(EStrand strn, int point, const CSeqScores &seqscr, const CExonParameters &params)

double Score(const CEResidueVec &seq, int i) const

CWAM_Stop(const objects::CGnomon_param::C_Param &from)

CMarkovChainArray< 1 > m_matrix

CWMM_Start(const objects::CGnomon_param::C_Param &from)

CMarkovChainArray< 0 > m_matrix

double Score(const CEResidueVec &seq, int i) const

container_type::const_iterator const_iterator

container_type::iterator iterator

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

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

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

#define ITERATE(Type, Var, Cont)

ITERATE macro to sequence through container elements.

#define NCBI_THROW(exception_class, err_code, message)

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

ESerialDataFormat

Data file format.

static CObjectIStream * Open(ESerialDataFormat format, CNcbiIstream &inStream, bool deleteInStream)

Create serial object reader and attach it to an input stream.

#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.

IO_PREFIX::istream CNcbiIstream

Portable alias for istream.

static const char label[]

list< double > TFirst_exon_phase_probabilities

TMin GetMin(void) const

Get the Min member data.

TL GetL(void) const

Get the L member data.

const TSingle_exon_length & GetSingle_exon_length(void) const

Get the Single_exon_length member data.

const TLast_exon_length & GetLast_exon_length(void) const

Get the Last_exon_length member data.

TA GetA(void) const

Get the A member data.

const Tdata & Get(void) const

Get the member data.

TStep GetStep(void) const

Get the Step member data.

const TRange & GetRange(void) const

Get the Range member data.

const TStop & GetStop(void) const

Get the variant data.

const TLength & GetLength(void) const

Get the Length member data.

const TInternal_exon_length & GetInternal_exon_length(void) const

Get the Internal_exon_length member data.

const TStart & GetStart(void) const

Get the variant data.

TIn_intron GetIn_intron(void) const

Get the In_intron member data.

TTo_term GetTo_term(void) const

Get the To_term member data.

const TIntron & GetIntron(void) const

Get the variant data.

const TFirst_exon_length & GetFirst_exon_length(void) const

Get the First_exon_length member data.

TTo_single GetTo_single(void) const

Get the To_single member data.

TIn_exon GetIn_exon(void) const

Get the In_exon member data.

const TP & GetP(void) const

Get the P member data.

TInitp GetInitp(void) const

Get the Initp member data.

const TFirst_exon_phase_probabilities & GetFirst_exon_phase_probabilities(void) const

Get the First_exon_phase_probabilities member data.

TMax GetMax(void) const

Get the Max member data.

list< double > TPhase_probabilities

E_Choice

Choice variants.

const TProbabilities & GetProbabilities(void) const

Get the Probabilities member data.

TInitp GetInitp(void) const

Get the Initp member data.

const TPhase_probabilities & GetPhase_probabilities(void) const

Get the Phase_probabilities member data.

const TLength & GetLength(void) const

Get the Length member data.

list< CRef< CGnomon_param > > Tdata

const TIntergenic & GetIntergenic(void) const

Get the variant data.

const TExon & GetExon(void) const

Get the variant data.

const TInternal_exon_phase_probabilities & GetInternal_exon_phase_probabilities(void) const

Get the Internal_exon_phase_probabilities member data.

TOrder GetOrder(void) const

Get the Order member data.

@ e_Coding_region

three elements (per phase)

void EvaluateInitialScore(State &r)

The blob sat and sat key Both must be positive integers</td > n< td > Non empty string The interpretation of the blob id depends on a processor Cassandra n processor expects the following format

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

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