42 #include "../../Text/TextTools.h"
43 #include "../Matrix/MatrixTools.h"
44 #include "../VectorTools.h"
57 for (
size_t i = 0; i < size; i++)
67 vSimplex_(hptm.vSimplex_)
73 AbstractParametrizable::operator=(hptm);
89 for (
size_t j = 0; j < pls.
size(); j++)
105 for (
size_t i = 0; i <
vSimplex_.size(); i++)
107 for (
size_t j = 0; j <
vSimplex_[i].dimension(); j++)
128 for (
size_t i = 0; i < salph; i++)
143 for (
size_t i = 0; i < salph; i++)
145 vSimplex_[i].matchParametersValues(parameters);
Partial implementation of HmmTransitionMatrix.
size_t getNumberOfStates() const
RowMatrix< double > tmpmat_
AbstractHmmTransitionMatrix & operator=(const AbstractHmmTransitionMatrix &hptm)
A partial implementation of the Parametrizable interface.
const ParameterList & getParameters() const
Get all parameters available.
virtual void addParameters_(const ParameterList ¶meters)
bool matchParametersValues(const ParameterList ¶meters)
Update the parameters from parameters.
Wrong size exception class.
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.
const Matrix< double > & getPij() const
Get all transition probabilities as a matrix.
The matrix template interface.
virtual std::vector< Scalar > row(size_t i) const =0
virtual size_t getNumberOfRows() const =0
The parameter list object.
virtual void addParameter(const Parameter ¶m)
Add a new parameter at the end of the list.
ParameterList * clone() const
Create a copy of this object and send a pointer to it.
This class is designed to facilitate the manipulation of parameters.
virtual void setName(const std::string &name)
Set the name of this parameter.
virtual const std::string & getName() const
Get the name of this parameter.
A Simplex object, used to define sets of probabilities that sum 1.
std::string toString(T t)
General template method to convert to a string.