src/algo/gnomon/hmm.hpp File Reference

#include <corelib/ncbistd.hpp>
#include <algo/gnomon/gnomon_exception.hpp>
#include <algo/gnomon/gnomon.hpp>
#include <algo/gnomon/gnomon__.hpp>
#include "gnomon_seq.hpp"
#include "score.hpp"

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Classes
class	CMarkovChain< order >
class	CMarkovChain< 0 >
class	CMarkovChainArray< order >
class	CInputModel
class	CTerminal
class	CWAM_Donor< order >
class	CWAM_Acceptor< order >
class	CWMM_Start
class	CWAM_Stop
class	CCodingRegion
class	CMC3_CodingRegion< order >
class	CNonCodingRegion
class	CMC_NonCodingRegion< order >
class	CNullRegion
struct	SStateScores
class	CLorentz
class	CHMM_State
class	CExonParameters
class	CExon
class	CSingleExon
class	CFirstExon
class	CInternalExon
class	CLastExon
class	CIntronParameters
class	CIntron
class	CIntergenicParameters
class	CIntergenic
class	CHMMParameters::SDetails
Functions
template<class State>
SStateScores	CalcStateScores (const State &st)
Variables
const double	kLnHalf
const double	kLnThree
const int	kTooFarLen = 500

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Function Documentation

template<class State> SStateScores CalcStateScores (  const State &  st  )

Definition at line 223 of file hmm.hpp. References SStateScores::m_length. Referenced by CIntergenic::GetStateScores(), CIntron::GetStateScores(), CLastExon::GetStateScores(), CInternalExon::GetStateScores(), CFirstExon::GetStateScores(), and CSingleExon::GetStateScores().

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Variable Documentation

const double kLnHalf

Definition at line 45 of file hmm.cpp. Referenced by CSingleExon::BranchScore(), and CLastExon::BranchScore().

const double kLnThree

Definition at line 46 of file hmm.cpp. Referenced by CSingleExon::LengthScore(), CFirstExon::LengthScore(), CInternalExon::LengthScore(), and CLastExon::LengthScore().

const int kTooFarLen = 500

Definition at line 47 of file hmm.hpp. Referenced by s_MakeStep(), and s_TooFar().

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