bpp::SimProcessEdge Class Reference

#include <Bpp/Phyl/Simulation/SimpleSubstitutionProcessSiteSimulator.h>

Inheritance diagram for bpp::SimProcessEdge:

Collaboration diagram for bpp::SimProcessEdge:

Public Member Functions
	SimProcessEdge (const ProcessComputationEdge &pce)
std::shared_ptr< const BranchModelInterface >	getModel () const
uint	getModelNumber () const
uint	getSpeciesIndex () const
const std::vector< uint > &	subModelNumbers () const
bool	useProb () const

Private Attributes
VVVdouble	cumpxy_
std::shared_ptr< const BranchModelInterface >	model_
	Model carried by the branch. More...
uint	nmodel_
	Number of the model carried by the branch. More...
std::vector< uint >	vSubNb_
	numbers of the submodels used, if any. More...
bool	useProb_
	use the probability associated to the edge in case of mixture. If true, the probability is used and not the transition probabilities. More...
const uint	speciesIndex_
	the index of the species in the phyloTree matching this node. More...

Friends
class	SimpleSubstitutionProcessSiteSimulator
class	GivenDataSubstitutionProcessSiteSimulator

Detailed Description

Definition at line 48 of file SimpleSubstitutionProcessSiteSimulator.h.

Constructor & Destructor Documentation

SimProcessEdge()

bpp::SimProcessEdge::SimProcessEdge ( const ProcessComputationEdge &  pce )

inline

Definition at line 56 of file SimpleSubstitutionProcessSiteSimulator.h.

Member Function Documentation

getModel()

std::shared_ptr<const BranchModelInterface> bpp::ProcessComputationEdge::getModel ( ) const

inlineinherited

Definition at line 130 of file ProcessComputationTree.h.

References bpp::ProcessComputationEdge::model_.

getModelNumber()

uint bpp::ProcessComputationEdge::getModelNumber ( ) const

inlineinherited

Definition at line 135 of file ProcessComputationTree.h.

References bpp::ProcessComputationEdge::nmodel_.

getSpeciesIndex()

uint bpp::ProcessComputationEdge::getSpeciesIndex ( ) const

inlineinherited

Definition at line 140 of file ProcessComputationTree.h.

References bpp::ProcessComputationEdge::speciesIndex_.

subModelNumbers()

const std::vector<uint>& bpp::ProcessComputationEdge::subModelNumbers ( ) const

inlineinherited

Definition at line 145 of file ProcessComputationTree.h.

References bpp::ProcessComputationEdge::vSubNb_.

useProb()

bool bpp::ProcessComputationEdge::useProb ( ) const

inlineinherited

Definition at line 150 of file ProcessComputationTree.h.

References bpp::ProcessComputationEdge::useProb_.

Friends And Related Function Documentation

GivenDataSubstitutionProcessSiteSimulator

friend class GivenDataSubstitutionProcessSiteSimulator

friend

Definition at line 60 of file SimpleSubstitutionProcessSiteSimulator.h.

SimpleSubstitutionProcessSiteSimulator

friend class SimpleSubstitutionProcessSiteSimulator

friend

Definition at line 59 of file SimpleSubstitutionProcessSiteSimulator.h.

Member Data Documentation

cumpxy_

VVVdouble bpp::SimProcessEdge::cumpxy_

private

Definition at line 53 of file SimpleSubstitutionProcessSiteSimulator.h.

model_

std::shared_ptr<const BranchModelInterface> bpp::ProcessComputationEdge::model_

privateinherited

Model carried by the branch.

Definition at line 81 of file ProcessComputationTree.h.

Referenced by bpp::ProcessComputationEdge::getModel().

nmodel_

uint bpp::ProcessComputationEdge::nmodel_

privateinherited

Number of the model carried by the branch.

Definition at line 86 of file ProcessComputationTree.h.

Referenced by bpp::ProcessComputationEdge::getModelNumber().

speciesIndex_

const uint bpp::ProcessComputationEdge::speciesIndex_

privateinherited

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

Definition at line 106 of file ProcessComputationTree.h.

Referenced by bpp::ProcessComputationEdge::getSpeciesIndex().

useProb_

bool bpp::ProcessComputationEdge::useProb_

privateinherited

use the probability associated to the edge in case of mixture. If true, the probability is used and not the transition probabilities.

Definition at line 101 of file ProcessComputationTree.h.

Referenced by bpp::ProcessComputationEdge::useProb().

vSubNb_

std::vector<uint> bpp::ProcessComputationEdge::vSubNb_

privateinherited

numbers of the submodels used, if any.

In practice, only vectors of size <=1 are implemented (ie individual submodels), to be fixed later.

Definition at line 94 of file ProcessComputationTree.h.

Referenced by bpp::ProcessComputationEdge::subModelNumbers().

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

• Bpp/Phyl/Simulation/SimpleSubstitutionProcessSiteSimulator.h