5 #ifndef BPP_PHYL_LIKELIHOOD_PHYLOLIKELIHOODS_SETOFALIGNEDPHYLOLIKELIHOOD_H
6 #define BPP_PHYL_LIKELIHOOD_PHYLOLIKELIHOODS_SETOFALIGNEDPHYLOLIKELIHOOD_H
70 std::shared_ptr<PhyloLikelihoodContainer> pC,
71 bool inCollection =
true,
72 const std::string& prefix =
"");
76 std::shared_ptr<PhyloLikelihoodContainer> pC,
77 const std::vector<size_t>& nPhylo,
78 bool inCollection =
true,
79 const std::string& prefix =
"");
112 return std::dynamic_pointer_cast<const AlignedPhyloLikelihoodInterface>((*
pPhyloCont_)[nPhyl]);
117 return std::dynamic_pointer_cast<AlignedPhyloLikelihoodInterface>((*
pPhyloCont_)[nPhyl]);
The AlignedPhyloLikelihoodSet abstract class.
AbstractAlignedPhyloLikelihoodSet & operator=(const AbstractAlignedPhyloLikelihoodSet &soap)
bool addPhyloLikelihood(size_t nPhyl, const std::string &suff) override
adds a PhyloLikelihood already stored in the m ap, iff it is an AlignedPhyloLikelihood of the same si...
double getLogLikelihoodForASiteForAPhyloLikelihood(size_t site, size_t nPhyl) const override
Get the log likelihood for a site for an aligned phyloLikelihood.
DataLik getLikelihoodForASiteForAPhyloLikelihood(size_t site, size_t nPhyl) const override
Get the likelihood for a site for an aligned phyloLikelihood.
AlignedPhyloLikelihoodInterface & alignedPhyloLikelihood(size_t nPhyl) override
AbstractAlignedPhyloLikelihoodSet(const AbstractAlignedPhyloLikelihoodSet &soap)
std::shared_ptr< const AlignedPhyloLikelihoodInterface > getAlignedPhyloLikelihood(size_t nPhyl) const override
virtual ~AbstractAlignedPhyloLikelihoodSet()
const AlignedPhyloLikelihoodInterface & alignedPhyloLikelihood(size_t nPhyl) const override
std::shared_ptr< AlignedPhyloLikelihoodInterface > getAlignedPhyloLikelihood(size_t nPhyl) override
AbstractAlignedPhyloLikelihoodSet(Context &context, std::shared_ptr< PhyloLikelihoodContainer > pC, bool inCollection=true, const std::string &prefix="")
AbstractAlignedPhyloLikelihood & operator=(const AbstractAlignedPhyloLikelihood &aasd)
The PhyloLikelihoodSet class, to manage a subset of PhyloLikelihoods from a given PhyloLikelihoodCont...
std::shared_ptr< PhyloLikelihoodContainer > pPhyloCont_
pointer to a PhyloLikelihoodContainer
AbstractPhyloLikelihoodSet & operator=(const AbstractPhyloLikelihoodSet &sd)
const Context & context() const override
The AlignedPhyloLikelihood interface, for phylogenetic likelihood.
virtual double getLogLikelihoodForASite(size_t site) const =0
Get the log likelihood for a site, and its derivatives.
virtual DataLik getLikelihoodForASite(size_t site) const =0
Get the likelihood for a site.
Joint interface SetOf+Aligned PhylLikelihood.
virtual double getLogLikelihoodForASiteForAPhyloLikelihood(size_t site, size_t nPhyl) const =0
Get the log likelihood for a site for an aligned phyloLikelihood.
virtual std::shared_ptr< AlignedPhyloLikelihoodInterface > getAlignedPhyloLikelihood(size_t nPhyl)=0
virtual const AlignedPhyloLikelihoodInterface & alignedPhyloLikelihood(size_t nPhyl) const =0
AlignedPhyloLikelihoodSetInterface * clone() const override=0
virtual AlignedPhyloLikelihoodInterface & alignedPhyloLikelihood(size_t nPhyl)=0
virtual DataLik getLikelihoodForASiteForAPhyloLikelihood(size_t site, size_t nPhyl) const =0
Get the likelihood for a site for an aligned phyloLikelihood.
virtual std::shared_ptr< const AlignedPhyloLikelihoodInterface > getAlignedPhyloLikelihood(size_t nPhyl) const =0
Context for dataflow node construction.
The PhyloLikelihoodSet interface, to manage a subset of PhyloLikelihoods from a given PhyloLikelihood...
Defines the basic types of data flow nodes.