40 #ifndef _DECOMPOSITIONREWARD_H_ 41 #define _DECOMPOSITIONREWARD_H_ 45 #include <Bpp/Numeric/Matrix/Matrix.h> 115 double getReward(
size_t initialState,
size_t finalState,
double length)
const;
131 void jFunction_(
const std::vector<double>& lambda,
double t, RowMatrix<double>& result)
const;
143 #endif // _DECOMPOSITIONREWARD_H_ RowMatrix< double > bMatrice_
RowMatrix< double > jMat_
Interface for all substitution models.
void alphabetIndexHasChanged()
RowMatrix< double > rewards_
virtual ~DecompositionReward()
DecompositionReward & operator=(const DecompositionReward &dr)
AbstractReward & operator=(const AbstractReward &ar)
Analytical reward using the eigen decomposition method.
Basic implementation of the the Reward interface.
DecompositionReward(const SubstitutionModel *model, AlphabetIndex1 *alphIndex)
Interface for reversible substitution models.
double getReward(size_t initialState, size_t finalState, double length) const
Get the reward of susbstitutions on a branch, given the initial and final states, and the branch leng...
const ReversibleSubstitutionModel * model_
void computeRewards_(double length) const
RowMatrix< double > insideProduct_
DecompositionReward(const DecompositionReward &dr)
void jFunction_(const std::vector< double > &lambda, double t, RowMatrix< double > &result) const
std::vector< double > lambda_
DecompositionReward * clone() const
Matrix< double > * getAllRewards(double length) const
Get the rewards on a branch, for each initial and final states, and given the branch length...
void setSubstitutionModel(const SubstitutionModel *model)
Set the substitution model.
RowMatrix< double > vInv_