5 #ifndef BPP_PHYL_LIKELIHOOD_PHYLOLIKELIHOODS_AUTOCORRELATIONOFALIGNEDPHYLOLIKELIHOOD_H
6 #define BPP_PHYL_LIKELIHOOD_PHYLOLIKELIHOODS_AUTOCORRELATIONOFALIGNEDPHYLOLIKELIHOOD_H
31 std::shared_ptr<HmmPhyloAlphabet>
hma_;
33 std::shared_ptr<AutoCorrelationTransitionMatrix>
htm_;
35 std::shared_ptr<HmmPhyloEmissionProbabilities>
hpep_;
37 mutable std::shared_ptr<HmmLikelihood_DF>
hmm_;
42 std::shared_ptr<PhyloLikelihoodContainer> pC,
43 const std::vector<size_t>& nPhylo,
44 bool inCollection =
true);
115 auto mat =
hmm_->getHiddenStatesPosteriorProbabilities().transpose();
123 auto mat =
hmm_->getHiddenStatesPosteriorProbabilitiesForASite(site);
130 return hmm_->getHmmTransitionMatrix();
The AlignedPhyloLikelihoodSet abstract class.
AbstractAlignedPhyloLikelihoodSet & operator=(const AbstractAlignedPhyloLikelihoodSet &soap)
The PhyloLikelihoodSet class, to manage a subset of PhyloLikelihoods from a given PhyloLikelihoodCont...
const Context & context() const override
Likelihood framework based on a hmm of simple likelihoods.
const Eigen::MatrixXd & getHmmTransitionMatrix() const
virtual ~AlignedPhyloLikelihoodAutoCorrelation()
VVdouble getPosteriorProbabilitiesPerSitePerAligned() const
void setNamespace(const std::string &nameSpace)
AlignedPhyloLikelihoodAutoCorrelation & operator=(const AlignedPhyloLikelihoodAutoCorrelation &mlc)
AlignedLikelihoodCalculation & alignedLikelihoodCalculation() const
std::shared_ptr< AutoCorrelationTransitionMatrix > htm_
AlignedPhyloLikelihoodAutoCorrelation(const AlignedPhyloLikelihoodAutoCorrelation &mlc)
std::shared_ptr< LikelihoodCalculation > getLikelihoodCalculation() const
LikelihoodCalculation & likelihoodCalculation() const
Vdouble getPosteriorProbabilitiesForASitePerAligned(size_t site) const
std::shared_ptr< HmmLikelihood_DF > hmm_
std::shared_ptr< AlignedLikelihoodCalculation > getAlignedLikelihoodCalculation() const
AlignedPhyloLikelihoodAutoCorrelation(Context &context, std::shared_ptr< PhyloLikelihoodContainer > pC, const std::vector< size_t > &nPhylo, bool inCollection=true)
std::shared_ptr< HmmPhyloEmissionProbabilities > hpep_
AlignedPhyloLikelihoodAutoCorrelation * clone() const
std::shared_ptr< HmmPhyloAlphabet > hma_
void fireParameterChanged(const ParameterList ¶meters)
Context for dataflow node construction.
Defines the basic types of data flow nodes.
std::vector< double > Vdouble
template void copyEigenToBpp(const ExtendedFloatMatrixXd &eigenMatrix, std::vector< std::vector< double >> &bppMatrix)
std::vector< Vdouble > VVdouble