#include <Bpp/Phyl/Likelihood/DataFlow/ProcessTree.h>

Collaboration diagram for bpp::ProcessEdge:

Public Member Functions
	ProcessEdge (uint speciesIndex, std::shared_ptr< ConfiguredParameter > brlen, std::shared_ptr< ConfiguredModel > model, std::shared_ptr< NumericConstant< size_t > > nMod=0)
	Construction with model and brlen. More...

	ProcessEdge (uint speciesIndex, ValueRef< double > brprob)
	Construction with probability ref from Mixture model. More...

	ProcessEdge (const ProcessEdge &edge)
	Copy construction. More...

std::shared_ptr< ConfiguredModel >	getModel ()

ConfiguredModel &	model ()

std::shared_ptr< ConfiguredParameter >	getBrLen ()

void	setBrLen (std::shared_ptr< ConfiguredParameter > brlen)

void	setTransitionMatrix (ValueRef< Eigen::MatrixXd > transitionMatrix)

ValueRef< Eigen::MatrixXd >	getTransitionMatrix ()

ValueRef< double >	getProba ()

std::shared_ptr< NumericConstant< size_t > >	getNMod ()

uint	getSpeciesIndex () const

Private Attributes
const Speciesindex	speciesIndex_
	the index of the species in the phyloTree matching this node. More...

std::shared_ptr< ConfiguredParameter >	brlen_
	Model & BrLen, = 0 if not supporting a model. More...

std::shared_ptr< ConfiguredModel >	model_

std::shared_ptr< NumericConstant< size_t > >	nMod_
	Optional number of submodels, in case model_ is mixed and a submodel is used. More...

ValueRef< Eigen::MatrixXd >	transitionMatrix_

ValueRef< double >	brprob_
	Probability of the edge, used in case of mixture models. More...

Detailed Description

Definition at line 37 of file ProcessTree.h.

Constructor & Destructor Documentation

◆ ProcessEdge() [1/3]

bpp::ProcessEdge::ProcessEdge	(	uint	speciesIndex,
		std::shared_ptr< ConfiguredParameter >	brlen,
		std::shared_ptr< ConfiguredModel >	model,
		std::shared_ptr< NumericConstant< size_t > >	nMod = `0`
	)

inline

Construction with model and brlen.

Definition at line 73 of file ProcessTree.h.

◆ ProcessEdge() [2/3]

bpp::ProcessEdge::ProcessEdge	(	uint	speciesIndex,
		ValueRef< double >	brprob
	)

inline

Construction with probability ref from Mixture model.

Definition at line 81 of file ProcessTree.h.

◆ ProcessEdge() [3/3]

bpp::ProcessEdge::ProcessEdge ( const ProcessEdge & edge )

inline

Copy construction.

Definition at line 87 of file ProcessTree.h.

Member Function Documentation

◆ getBrLen()

std::shared_ptr< ConfiguredParameter > bpp::ProcessEdge::getBrLen ( )

inline

Definition at line 104 of file ProcessTree.h.

References brlen_.

◆ getModel()

std::shared_ptr< ConfiguredModel > bpp::ProcessEdge::getModel ( )

inline

Definition at line 89 of file ProcessTree.h.

References model_.

◆ getNMod()

std::shared_ptr< NumericConstant< size_t > > bpp::ProcessEdge::getNMod ( )

inline

Definition at line 134 of file ProcessTree.h.

References nMod_.

◆ getProba()

ValueRef< double > bpp::ProcessEdge::getProba ( )

inline

Definition at line 124 of file ProcessTree.h.

References brprob_.

◆ getSpeciesIndex()

uint bpp::ProcessEdge::getSpeciesIndex ( ) const

inline

Definition at line 139 of file ProcessTree.h.

References speciesIndex_.

◆ getTransitionMatrix()

ValueRef< Eigen::MatrixXd > bpp::ProcessEdge::getTransitionMatrix ( )

inline

Definition at line 119 of file ProcessTree.h.

References transitionMatrix_.

◆ model()

ConfiguredModel & bpp::ProcessEdge::model ( )

inline

Definition at line 94 of file ProcessTree.h.

References model_.

◆ setBrLen()

void bpp::ProcessEdge::setBrLen ( std::shared_ptr< ConfiguredParameter > brlen )

inline

Definition at line 109 of file ProcessTree.h.

References brlen_.

◆ setTransitionMatrix()

void bpp::ProcessEdge::setTransitionMatrix ( ValueRef< Eigen::MatrixXd > transitionMatrix )

inline

Definition at line 114 of file ProcessTree.h.

References transitionMatrix_.

Member Data Documentation

◆ brlen_

std::shared_ptr<ConfiguredParameter> bpp::ProcessEdge::brlen_

private

Model & BrLen, = 0 if not supporting a model.

Definition at line 48 of file ProcessTree.h.

Referenced by getBrLen(), and setBrLen().

◆ brprob_

ValueRef<double> bpp::ProcessEdge::brprob_

private

Probability of the edge, used in case of mixture models.

Definition at line 67 of file ProcessTree.h.

Referenced by getProba().

◆ model_

std::shared_ptr<ConfiguredModel> bpp::ProcessEdge::model_

private

Definition at line 50 of file ProcessTree.h.

Referenced by getModel(), and model().

◆ nMod_

std::shared_ptr<NumericConstant<size_t> > bpp::ProcessEdge::nMod_

private

Optional number of submodels, in case model_ is mixed and a submodel is used.

Definition at line 60 of file ProcessTree.h.

Referenced by getNMod().

◆ speciesIndex_

const Speciesindex bpp::ProcessEdge::speciesIndex_

private

the index of the species in the phyloTree matching this node.

Definition at line 43 of file ProcessTree.h.

Referenced by getSpeciesIndex().

◆ transitionMatrix_

ValueRef<Eigen::MatrixXd> bpp::ProcessEdge::transitionMatrix_

private

Definition at line 62 of file ProcessTree.h.

Referenced by getTransitionMatrix(), and setTransitionMatrix().

The documentation for this class was generated from the following file:

Bpp/Phyl/Likelihood/DataFlow/ProcessTree.h

Public Member Functions

Private Attributes

Detailed Description

Constructor & Destructor Documentation

◆ ProcessEdge() [1/3]

◆ ProcessEdge() [2/3]

◆ ProcessEdge() [3/3]

Member Function Documentation

◆ getBrLen()

◆ getModel()

◆ getNMod()

◆ getProba()

◆ getSpeciesIndex()

◆ getTransitionMatrix()

◆ model()

◆ setBrLen()

◆ setTransitionMatrix()

Member Data Documentation

◆ brlen_

◆ brprob_

◆ model_

◆ nMod_

◆ speciesIndex_

◆ transitionMatrix_