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Showing content from http://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/doxyhtml/hmm_8hpp_source.html below:

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

1 #ifndef ALGO_GNOMON___HMM__HPP 2 #define ALGO_GNOMON___HMM__HPP 54 void InitScore

(

const

objects::CMarkov_chain_params& hmm_param_asn);

63 void Init

(

const

objects::CMarkov_chain_params& hmm_param_asn);

72 void InitScore

(

const

objects::CMarkov_chain_params& from);

80 void Init

(

const

objects::CMarkov_chain_params& from);

88 void InitScore

(

int l

const

objects::CMarkov_chain_array& from);

92

vector< CMarkovChain<order> >

m_mc

;

127 CWAM_Donor

(

const

objects::CGnomon_param::C_Param& from);

138 CWAM_Acceptor

(

const

objects::CGnomon_param::C_Param& from);

151 CWMM_Start

(

const

objects::CGnomon_param::C_Param& from);

162 static string class_id

() {

return "WAM_Stop_1"

; }

163 CWAM_Stop

(

const

objects::CGnomon_param::C_Param& from);

174 static string class_id

() {

return "CodingRegion"

; }

194 static string class_id

() {

return "NonCodingRegion"

; }

227 if

(

.NoLeftEnd())

229 if

(

.NoRightEnd()) sc.

m_length

.ThroughLengthScore();

234 if

(

.NoRightEnd()) sc.

m_length

.ClosingLengthScore();

242 if

(

.LeftState()) sc.

m_score

.LeftState()->Score();

251 void Init

(

const

objects::CLength_distribution_params& from);

257 double Through

(

int

seqlen)

const

;

293 virtual bool isExon

()

const

{

return false

; }

338 virtual bool isExon

()

const

{

return true

; }

500 int

shift =

.Stop()-

.Start();

501 if

((

Phase

()+shift)%3 ==

.Phase())

515 if

((ph+1)%3 ==

.Phase())

return

521 static string class_id

() {

return "Intergenic"

; }

563 SDetails

(

const

objects::CGnomon_params& hmm_params_asn);

567 template

class

CParam>

568 void ReadParameters

(

const

objects::CGnomon_params& hmm_params_asn, objects::CGnomon_param::C_Param::E_Choice choice);

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

double m_internalphase[3][3]

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

double InitialLengthScore() const

void UpdatePrevExon(const CExon &e)

const CExonParameters * m_param

double ClosingLengthScore() const

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

virtual bool isExon() const

double ThroughLengthScore() const

virtual bool isGeneLeftEnd() const

virtual bool isGeneRightEnd() const

double BranchScore(const CHMM_State &) const

virtual double VirtTermScore() const

string GetStateName() const

const CFirstExon * PrevExon() const

SStateScores GetStateScores() const

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

double LengthScore() const

void DeleteAllCreatedModels()

map< string, TCGContentList > TParamMap

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)

vector< CInputModel * > all_created_models

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

const CSeqScores * m_seqscr

const CSeqScores & GetSeqScores() const

virtual bool isGeneRightEnd() const

const CHMM_State * LeftState() const

virtual string GetStateName() const =0

virtual double VirtTermScore() const =0

const CTerminal * TerminalPtr() const

const CTerminal * m_terminal

virtual SStateScores GetStateScores() const =0

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

void UpdateLeftState(const CHMM_State &left)

void UpdateScore(double scr)

virtual bool isGeneLeftEnd() const

const CHMM_State * m_leftstate

virtual bool isExon() const

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 LengthScore() const

double ClosingLengthScore() const

double BranchScore(const CHMM_State &) const

const CIntergenicParameters * m_param

virtual double VirtTermScore() const

string GetStateName() const

SStateScores GetStateScores() const

double ThroughLengthScore() const

double InitialLengthScore() const

double BranchScore(const CHMM_State &) const

double LengthScore() const

SStateScores GetStateScores() const

string GetStateName() const

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

virtual double VirtTermScore() const

const CInternalExon * PrevExon() const

void SetSeqLen(int seqlen) const

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

bool SplittedStop() const

SStateScores GetStateScores() const

const CIntronParameters * m_param

double BranchScore(const CHMM_State &) const

double InitialLengthScore() const

double LengthScore() 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 ThroughLengthScore() const

double ClosingLengthScore() const

string GetStateName() const

virtual double VirtTermScore() const

double LengthScore() const

SStateScores GetStateScores() const

string GetStateName() const

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

virtual double VirtTermScore() const

virtual bool isGeneLeftEnd() const

double BranchScore(const CHMM_State &) const

virtual bool isGeneRightEnd() const

const CLastExon * PrevExon() const

double Score(int l) const

void Init(const objects::CLength_distribution_params &from)

double Through(int seqlen) const

double ClosingScore(int l) const

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

CMarkovChain< order > m_matrix[3]

CMC3_CodingRegion(const objects::CGnomon_param::C_Param &from)

CMarkovChain< order > m_matrix

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

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

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

vector< CMarkovChain< order > > m_mc

double Score(const EResidue *seq) const

const double & Score(const EResidue *seq) const

double & Score(const EResidue *seq)

void Init(const objects::CMarkov_chain_params &hmm_param_asn)

CMarkovChain< order-1 > & SubChain(int i)

CMarkovChain< order > Type

CMarkovChain< order-1 > m_next[5]

const double & Score(const EResidue *seq) const

double & Score(const EResidue *seq)

void InitScore(const objects::CMarkov_chain_params &hmm_param_asn)

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

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

double Score(const CEResidueVec &, int) const

double AcceptorScore(int i, int strand) const

double DonorScore(int i, int strand) const

bool SplittedStop(int id, int ia, int strand, int ph) const

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

virtual bool isGeneRightEnd() const

string GetStateName() const

SStateScores GetStateScores() const

double BranchScore(const CHMM_State &) const

virtual double VirtTermScore() const

virtual bool isGeneLeftEnd() const

double LengthScore() const

const CSingleExon * PrevExon() const

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

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

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

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

CMarkovChainArray< order > m_matrix

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

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

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

Include a standard set of the NCBI C++ Toolkit most basic headers.

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

#define NCBI_THROW(exception_class, err_code, message)

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

#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.

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.

static const char label[]

unsigned int

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

SStateScores CalcStateScores(const State &st)

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

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

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