41 #ifndef BPP_NUMERIC_HMM_FULLHMMTRANSITIONMATRIX_H
42 #define BPP_NUMERIC_HMM_FULLHMMTRANSITIONMATRIX_H
45 #include "../AbstractParameterAliasable.h"
46 #include "../Prob/Simplex.h"
95 double Pij(
size_t i,
size_t j)
const
Partial implementation of HmmTransitionMatrix.
A partial implementation of the Parametrizable interface.
Describe the transition probabilities between hidden states of a Hidden Markov Model.
std::vector< Simplex > vSimplex_
const std::vector< double > & getEquilibriumFrequencies() const
FullHmmTransitionMatrix(const HmmStateAlphabet *alph, const std::string &prefix="")
void fireParameterChanged(const ParameterList ¶meters)
Notify the class when one or several parameters have changed.
FullHmmTransitionMatrix & operator=(const FullHmmTransitionMatrix &hptm)
void setTransitionProbabilities(const Matrix< double > &mat)
Set the matrix of the transition probabilities.
double Pij(size_t i, size_t j) const
Get the transition probability between two states.
const Matrix< double > & getPij() const
Get all transition probabilities as a matrix.
FullHmmTransitionMatrix * clone() const
Create a copy of this object and send a pointer to it.
The matrix template interface.
The parameter list object.