Inheritance diagram for ExonEvo:

Public Member Functions
	ExonEvo (int num_states=2)

	ExonEvo (int num_states, double lambda, double mu, double ali_error)

void	setPi ()

void	setLambda (double lambda=0.0001, bool propsOverride=true)

void	setMu (double mu=0.0001, bool propsOverride=true)

void	setAliErr (double ali_error=0.1, bool propsOverride=true)

double	getLambda () const

double	getMu () const

double	getAliErr () const

void	getRateMatrices ()

void	computeLogPmatrices ()

void	addBranchLength (double b)

double	minBranchLength () const

int	eigendecompose (gsl_matrix *Q)

gsl_matrix *	expQt (double t)

gsl_matrix *	getExonRateMatrix ()

void	validateEigenDecomp (gsl_matrix *Q)

Public Member Functions inherited from Evo
	Evo (int s)

int	getNumStates ()

void	setBranchLengths (vector< double > b, int m=-1)

void	printBranchLengths ()

double	getPi (int i) const

double	getLogPi (int i) const

gsl_matrix *	getSubMatrixQ (int u)

gsl_matrix *	getSubMatrixP (int u, double t)

gsl_matrix *	getSubMatrixLogP (int u, double t)

gsl_matrix *	expQt (double t, gsl_vector lambda, gsl_matrix U, gsl_matrix *Uinv)

Additional Inherited Members
Protected Member Functions inherited from Evo
int	findClosestIndex (vector< double > &v, double val)

Protected Attributes inherited from Evo
const int	states

int	m

double *	pi

vector< double >	times

vector< gsl_matrix * >	allQs

Matrix< gsl_matrix * >	allPs

Matrix< gsl_matrix * >	allLogPs

Member Function Documentation

◆ addBranchLength()

void ExonEvo::addBranchLength ( double b )

virtual

Implements Evo.

void ExonEvo::computeLogPmatrices ( )

virtual

Implements Evo.

void ExonEvo::getRateMatrices ( )

virtual

Reimplemented from Evo.

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