41 #ifndef BPP_NUMERIC_HMM_HMMTRANSITIONMATRIX_H
42 #define BPP_NUMERIC_HMM_HMMTRANSITIONMATRIX_H
45 #include "../Matrix/Matrix.h"
46 #include "../Parametrizable.h"
89 virtual double Pij(
size_t i,
size_t j)
const = 0;
Describe the transition probabilities between hidden states of a Hidden Markov Model.
virtual void setHmmStateAlphabet(const HmmStateAlphabet *stateAlphabet)=0
Set the new hidden state alphabet.
virtual size_t getNumberOfStates() const =0
virtual const Matrix< double > & getPij() const =0
Get all transition probabilities as a matrix.
virtual const std::vector< double > & getEquilibriumFrequencies() const =0
virtual const HmmStateAlphabet * getHmmStateAlphabet() const =0
virtual double Pij(size_t i, size_t j) const =0
Get the transition probability between two states.
The matrix template interface.
This is the interface for all objects that imply parameters.