ForwardLikelihoodTree.h File Reference

#include <Bpp/Graph/AssociationDAGraphImplObserver.h>
#include <Bpp/Seq/Container/AlignmentData.h>
#include "Bpp/Phyl/Likelihood/DataFlow/ProcessTree.h"
#include "Definitions.h"

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Classes
class	bpp::ForwardLikelihoodTree
class	bpp::ProbabilityDAG

Namespaces
	bpp
	Defines the basic types of data flow nodes.

Typedefs
using	bpp::SpeciationForward = CWiseMul< MatrixLik, ReductionOf< MatrixLik > >
using	bpp::MixtureForward = CWiseAdd< MatrixLik, ReductionOf< MatrixLik > >
using	bpp::ForwardTransition = MatrixProduct< MatrixLik, Eigen::MatrixXd, MatrixLik >
	forwardLikelihood = f(transitionMatrix, conditionalLikelihood). More...
using	bpp::ForwardTransitionFunction = CWiseApply< MatrixLik, MatrixLik, TransitionFunction >
using	bpp::ForwardProportion = CWiseMul< MatrixLik, std::tuple< double, MatrixLik > >
	forwardLikelihood = f(transitionMatrix, proportion). More...
using	bpp::ConditionalLikelihoodForward = Value< MatrixLik >
	Interface LikelihoodTree data structure. More...
using	bpp::ConditionalLikelihoodForwardRef = ValueRef< MatrixLik >
using	bpp::ForwardLikelihoodBelow = Value< MatrixLik >
using	bpp::ForwardLikelihoodBelowRef = ValueRef< MatrixLik >
using	bpp::DAGindexes = std::vector< uint >
	Helper: create a map with mutable dataflow nodes for each branch of the tree. The map is indexed by branch ids. More...
using	bpp::Speciesindex = uint
using	bpp::Proba = Value< double >
	DAG with the same shape as ForwardLikelihoodTree with computations of probabilities of nodes & branches. More...
using	bpp::ProbaRef = std::shared_ptr< Value< double > >
using	bpp::DAProb = AssociationDAGlobalGraphObserver< Proba, Proba >
using	bpp::ProbaMul = CWiseMul< double, std::tuple< double, double > >
using	bpp::ProbaSum = CWiseAdd< double, ReductionOf< double > >

Functions
Dimension< TransitionFunction >	bpp::transitionFunctionDimension (Eigen::Index nbState)
MatrixDimension	bpp::conditionalLikelihoodDimension (Eigen::Index nbState, Eigen::Index nbSite)