Maintains parameter for computing match probabilities. More...

Collaboration diagram for LocARNA::PairHMMMatchProbs::PairHMMParams:

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Public Member Functions
	PairHMMParams (const std::string &filename)

Public Attributes
double	initM
	transition probability initM

double	initX
	transition probability initX

double	initY
	transition probability initY

double	startX
	transition probability startX

double	startY
	transition probability startY

double	extendM
	transition probability extendM

double	extendX
	transition probability extendX

double	extendY
	transition probability extendY

double	startMFromX
	transition probability startMFromX

double	startMFromY
	transition probability startMFromY

std::string	basenames
	base names

Matrix< double >	emmission
	matrix of emmission probabilities

std::vector< double >	background
	vector of background probabilities

Detailed Description

Maintains parameter for computing match probabilities.

The class is used in sequence alignment a la Probcons by MatchProbs::pairHMM_probs()

Supports reading parameter from file

Constructor & Destructor Documentation

LocARNA::PairHMMMatchProbs::PairHMMParams::PairHMMParams ( const std::string & filename )

explicit

Construct from file

Parameters

filename

Exceptions

failure

The documentation for this class was generated from the following files: