15 HmmProcessPhyloLikelihood::HmmProcessPhyloLikelihood(
16 std::shared_ptr<const AlignmentDataInterface> data,
17 std::shared_ptr<HmmSequenceEvolution> processSeqEvol,
18 std::shared_ptr<CollectionNodes> collNodes,
25 data->getNumberOfSites(),
26 (processSeqEvol->getSubstitutionProcessNumbers().size() != 0)
27 ? processSeqEvol->substitutionProcess(processSeqEvol->getSubstitutionProcessNumbers()[0]).getNumberOfStates()
36 auto alphyl = make_shared<HmmPhyloAlphabet>(*
this);
38 Hpep_ = make_shared<HmmPhyloEmissionProbabilities>(alphyl);
40 hmm_ = make_shared<HmmLikelihood_DF>(
context(), processSeqEvol->getHmmProcessAlphabet(), processSeqEvol->getHmmTransitionMatrix(),
Hpep_);
48 hmm_->setNamespace(nameSpace);
54 hmm_->matchParametersValues(parameters);
virtual void fireParameterChanged(const ParameterList ¶meters) override
void setNamespace(const std::string &nameSpace) override
virtual void addParameters_(const ParameterList ¶meters)
const Context & context() const override
void fireParameterChanged(const ParameterList ¶meters) override
std::shared_ptr< HmmPhyloEmissionProbabilities > Hpep_
std::shared_ptr< HmmLikelihood_DF > hmm_
LikelihoodCalculation in context of HMM.
void setNamespace(const std::string &nameSpace) override
Partial implementation of the Likelihood interface for multiple processes.
Defines the basic types of data flow nodes.