5 #ifndef BPP_PHYL_MAPPING_PHYLOMAPPINGS_SINGLEPROCESSSUBSTITUTIONMAPPING_H
6 #define BPP_PHYL_MAPPING_PHYLOMAPPINGS_SINGLEPROCESSSUBSTITUTIONMAPPING_H
9 #include "../../Likelihood/PhyloLikelihoods/SingleProcessPhyloLikelihood.h"
10 #include "../ProbabilisticSubstitutionMapping.h"
11 #include "../SubstitutionMappingTools.h"
27 public std::enable_shared_from_this<SingleProcessSubstitutionMapping>
30 std::shared_ptr<SingleProcessPhyloLikelihood>
pSPP_;
40 std::shared_ptr<SingleProcessPhyloLikelihood> spp,
41 std::shared_ptr<SubstitutionRegisterInterface> reg,
42 std::shared_ptr<const AlphabetIndex2> weights,
43 std::shared_ptr<const AlphabetIndex2> distances,
44 double threshold = -1,
101 return pSPP_->substitutionProcess().getNumberOfModels();
106 return pSPP_->substitutionProcess().getModelNumbers();
111 return pSPP_->likelihoodCalculationSingleProcess();
116 return pSPP_->likelihoodCalculationSingleProcess();
The AbstractSinglePhyloSubstitutionMapping class: substitution mapping linked with a Single Process P...
AbstractSinglePhyloSubstitutionMapping & operator=(const AbstractSinglePhyloSubstitutionMapping &sppm)
std::shared_ptr< const AlphabetIndex2 > getWeights() const
std::shared_ptr< const SubstitutionRegisterInterface > getSubstitutionRegister() const
std::shared_ptr< const AlphabetIndex2 > getDistances() const
std::unique_ptr< ProbabilisticSubstitutionMapping > counts_
The SingleProcessSubstitutionMapping class: substitution mapping linked with a SingleProcessPhyloLike...
size_t getNumberOfModels() const
virtual ~SingleProcessSubstitutionMapping()
SingleProcessSubstitutionMapping(std::shared_ptr< SingleProcessPhyloLikelihood > spp, std::shared_ptr< SubstitutionRegisterInterface > reg, std::shared_ptr< const AlphabetIndex2 > weights, std::shared_ptr< const AlphabetIndex2 > distances, double threshold=-1, bool verbose=true)
std::shared_ptr< SingleProcessPhyloLikelihood > pSPP_
SingleProcessSubstitutionMapping & operator=(const SingleProcessSubstitutionMapping &sppm)
std::vector< size_t > getModelNumbers() const
void computeCounts(short unresolvedOption=SubstitutionMappingTools::UNRESOLVED_ZERO, double threshold=-1, bool verbose=true)
ComputeCounts.
LikelihoodCalculationSingleProcess & getLikelihoodCalculationSingleProcess()
void setBranchedModelSet_()
Set the models of the BranchedModelSet to the adhoc branches, for normalization.
const LikelihoodCalculationSingleProcess & getLikelihoodCalculationSingleProcess() const
SingleProcessSubstitutionMapping * clone() const
void computeNormalizations(const ParameterList &nullParams, short unresolvedOption=SubstitutionMappingTools::UNRESOLVED_ZERO, bool verbose=true)
compute Normalizations
SingleProcessSubstitutionMapping(const SingleProcessSubstitutionMapping &sppm)
Defines the basic types of data flow nodes.