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