Evo Class Reference

abstract base class for codon and exon evolution More...

#include <contTimeMC.hh>

Inheritance diagram for Evo:

Public Member Functions
	Evo (int s)
int	getNumStates ()
void	setBranchLengths (vector< double > b, int m=-1)
void	printBranchLengths ()
virtual void	getRateMatrices ()
virtual void	computeLogPmatrices ()=0
virtual void	addBranchLength (double b)=0
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)

Protected Member Functions
int	findClosestIndex (vector< double > &v, double val)

Protected Attributes
const int	states
int	m
double *	pi
vector< double >	times
vector< gsl_matrix * >	allQs
Matrix< gsl_matrix * >	allPs
Matrix< gsl_matrix * >	allLogPs

Detailed Description

abstract base class for codon and exon evolution

Author

Mario Stanke

Stefanie König

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

• include/contTimeMC.hh
• src/contTimeMC.cc