104 mutable RowMatrix<double>
p_;
124 AbstractParameterAliasable(model),
139 AbstractParameterAliasable::operator=(model);
159 double Pij_t (
size_t i,
size_t j,
double d)
const;
160 double dPij_dt (
size_t i,
size_t j,
double d)
const;
161 double d2Pij_dt2(
size_t i,
size_t j,
double d)
const;
162 const Matrix<double>&
getPij_t (
double d)
const;
163 const Matrix<double>&
getdPij_dt (
double d)
const;
166 std::string
getName()
const {
return "RE08"; }
181 AbstractParameterAliasable::fireParameterChanged(parameters);
183 lambda_ = getParameter_(0).getValue();
184 mu_ = getParameter_(1).getValue();
190 double getInitValue(
size_t i,
int state)
const throw (IndexOutOfBoundsException, BadIntException);
const Matrix< double > & getd2Pij_dt2(double d) const
Interface for all substitution models.
RE08 & operator=(const RE08 &model)
void setNamespace(const std::string &prefix)
std::string getName() const
Get the name of the model.
const Matrix< double > & getPij_t(double d) const
RowMatrix< double > simpleGenerator_
void setFreqFromData(const SequenceContainer &data, double pseudoCount=0)
This method is forwarded to the simple model.
size_t getNumberOfStates() const
Get the number of states.
void fireParameterChanged(const ParameterList ¶meters)
Tells the model that a parameter value has changed.
const Matrix< double > & getdPij_dt(double d) const
void updateMatrices()
Compute and diagonalize the matrix, and fill the eigenValues_, leftEigenVectors_ and rightEigenVecto...
AbstractSubstitutionModel & operator=(const AbstractSubstitutionModel &model)
Partial implementation of the ReversibleSubstitutionModel interface.
const SubstitutionModel * getNestedModel() const
double d2Pij_dt2(size_t i, size_t j, double d) const
Interface for reversible substitution models.
RowMatrix< double > simpleExchangeabilities_
size_t size_
The size of the generator, i.e. the number of states.
double dPij_dt(size_t i, size_t j, double d) const
RE08(ReversibleSubstitutionModel *simpleModel, double lambda=0, double mu=0)
Build a new Rivas & Eddy model from a standard substitution model.
std::string nestedPrefix_
double getInitValue(size_t i, int state) const
The Rivas-Eddy substitution model with gap characters.
std::auto_ptr< ReversibleSubstitutionModel > simpleModel_
double Pij_t(size_t i, size_t j, double d) const