40 #ifndef _BINARYSUBSTITUTIONMODEL_H_ 41 #define _BINARYSUBSTITUTIONMODEL_H_ 44 #include <Bpp/Seq/Alphabet/BinaryAlphabet.h> 122 mutable RowMatrix<double>
p_;
133 double Pij_t (
size_t i,
size_t j,
double d)
const;
134 double dPij_dt (
size_t i,
size_t j,
double d)
const;
135 double d2Pij_dt2(
size_t i,
size_t j,
double d)
const;
136 const Matrix<double>&
getPij_t (
double d)
const;
137 const Matrix<double>&
getdPij_dt (
double d)
const;
140 std::string
getName()
const {
return "Binary"; }
142 void setFreq(std::map<int, double>& freqs);
151 #endif // _BINARYSUBSTITUTIONMODEL_H_ std::string getName() const
Get the name of the model.
const Matrix< double > & getdPij_dt(double d) const
const Matrix< double > & getd2Pij_dt2(double d) const
double dPij_dt(size_t i, size_t j, double d) const
const Matrix< double > & getPij_t(double d) const
size_t getNumberOfStates() const
Get the number of states.
BinarySubstitutionModel(const BinaryAlphabet *alpha, double kappa=1.)
Partial implementation of the ReversibleSubstitutionModel interface.
double Pij_t(size_t i, size_t j, double d) const
void setFreq(std::map< int, double > &freqs)
Set equilibrium frequencies.
void updateMatrices()
Compute and diagonalize the matrix, and fill the eigenValues_, leftEigenVectors_ and rightEigenVecto...
virtual ~BinarySubstitutionModel()
double d2Pij_dt2(size_t i, size_t j, double d) const
BinarySubstitutionModel * clone() const