40 #ifndef _WORDSUBSTITUTIONMODEL_H_ 41 #define _WORDSUBSTITUTIONMODEL_H_ 44 #include <Bpp/Numeric/Matrix/Matrix.h> 45 #include <Bpp/BppVector.h> 89 WordSubstitutionModel(
const std::vector<SubstitutionModel*>& modelVector,
const std::string& prefix =
"");
118 virtual const RowMatrix<double>&
getPij_t(
double d)
const;
120 virtual const RowMatrix<double>&
getdPij_dt(
double d)
const;
122 virtual const RowMatrix<double>&
getd2Pij_dt2(
double d)
const;
124 virtual std::string
getName()
const;
128 #endif // _WORDSUBSTITUTIONMODEL Interface for all substitution models.
virtual const RowMatrix< double > & getPij_t(double d) const
virtual void completeMatrices()
Called by updateMatrices to handle specific modifications for inheriting classes. ...
virtual const RowMatrix< double > & getd2Pij_dt2(double d) const
Abstract Basal class for words of substitution models.
virtual const RowMatrix< double > & getdPij_dt(double d) const
virtual std::string getName() const
Get the name of the model.
Basal class for words of reversible substitution models.
virtual ~WordSubstitutionModel()
virtual void updateMatrices()
Diagonalize the matrix, and fill the eigenValues_, iEigenValues_, leftEigenVectors_ and rightEigenVe...
WordSubstitutionModel(const std::vector< SubstitutionModel *> &modelVector, const std::string &prefix="")
Build a new WordSubstitutionModel object from a Vector of pointers to SubstitutionModels.
Map the states of a given alphabet which have a model state.
WordSubstitutionModel * clone() const