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

Inheritance diagram for bpp::SimProcessNode:

Collaboration diagram for bpp::SimProcessNode:

Public Member Functions
	SimProcessNode (const ProcessComputationNode &pcn)

uint	getSpeciesIndex () const

bool	isSpeciation () const

bool	isMixture () const

PhyloNode *	clone () const

Name:
std::string	getName () const
	Get the name associated to this node, if there is one, otherwise throw a NodeException. More...

void	setName (const std::string &name)
	Give a name or update the name associated to the node. More...

void	deleteName ()
	Delete the name associated to this node (do nothing if there is no name). More...

bool	hasName () const
	Tell is this node has a name. More...

Node properties:
void	setProperty (const std::string &name, const Clonable &property)
	Set/add a node property. More...

Clonable *	getProperty (const std::string &name)

const Clonable *	getProperty (const std::string &name) const

Clonable *	removeProperty (const std::string &name)

void	deleteProperty (const std::string &name)

void	removeProperties ()
	Remove all node properties. More...

void	deleteProperties ()
	Delete all node properties. More...

bool	hasProperty (const std::string &name) const

std::vector< std::string >	getPropertyNames () const

Private Attributes
size_t	state_

VVdouble	cumProb_

std::vector< std::shared_ptr< SimProcessNode > >	sons_

const uint	speciesIndex_
	the index of the species in the phyloTree matching this node. More...

std::string	name_

std::map< std::string, Clonable * >	properties_

Friends
class	SimpleSubstitutionProcessSiteSimulator

class	GivenDataSubstitutionProcessSiteSimulator

Detailed Description

Definition at line 27 of file SimpleSubstitutionProcessSiteSimulator.h.

Constructor & Destructor Documentation

◆ SimProcessNode()

bpp::SimProcessNode::SimProcessNode ( const ProcessComputationNode & pcn )

inline

Definition at line 41 of file SimpleSubstitutionProcessSiteSimulator.h.

Member Function Documentation

◆ clone()

PhyloNode* bpp::PhyloNode::clone ( ) const

inlineinherited

Definition at line 102 of file PhyloNode.h.

References bpp::PhyloNode::PhyloNode().

◆ deleteName()

void bpp::PhyloNode::deleteName ( )

inlineinherited

Delete the name associated to this node (do nothing if there is no name).

Definition at line 145 of file PhyloNode.h.

References bpp::PhyloNode::name_.

◆ deleteProperties()

void bpp::PhyloNode::deleteProperties ( )

inlineinherited

Delete all node properties.

Definition at line 234 of file PhyloNode.h.

References bpp::PhyloNode::properties_.

Referenced by bpp::PhyloNode::~PhyloNode().

◆ deleteProperty()

void bpp::PhyloNode::deleteProperty ( const std::string & name )

inlineinherited

Definition at line 210 of file PhyloNode.h.

References bpp::PhyloNode::hasProperty(), and bpp::PhyloNode::properties_.

◆ getName()

std::string bpp::PhyloNode::getName ( ) const

inlineinherited

Get the name associated to this node, if there is one, otherwise throw a NodeException.

Returns: The name associated to this node.

Definition at line 126 of file PhyloNode.h.

References bpp::PhyloNode::hasName(), and bpp::PhyloNode::name_.

◆ getProperty() [1/2]

Clonable* bpp::PhyloNode::getProperty ( const std::string & name )

inlineinherited

Definition at line 182 of file PhyloNode.h.

References bpp::PhyloNode::hasProperty(), and bpp::PhyloNode::properties_.

Referenced by bpp::StochasticMapping::getNodeState(), bpp::ProcessComputationNode::isMixture(), and bpp::ProcessComputationNode::isSpeciation().

◆ getProperty() [2/2]

const Clonable* bpp::PhyloNode::getProperty ( const std::string & name ) const

inlineinherited

Definition at line 190 of file PhyloNode.h.

References bpp::PhyloNode::hasProperty(), and bpp::PhyloNode::properties_.

◆ getPropertyNames()

std::vector<std::string> bpp::PhyloNode::getPropertyNames ( ) const

inlineinherited

Definition at line 245 of file PhyloNode.h.

References bpp::MapTools::getKeys(), and bpp::PhyloNode::properties_.

◆ getSpeciesIndex()

uint bpp::ProcessComputationNode::getSpeciesIndex ( ) const

inlineinherited

Definition at line 49 of file ProcessComputationTree.h.

References bpp::ProcessComputationNode::speciesIndex_.

Referenced by bpp::ProcessComputationNode::isMixture(), and bpp::ProcessComputationNode::isSpeciation().

◆ hasName()

bool bpp::PhyloNode::hasName ( ) const

inlineinherited

Tell is this node has a name.

Returns: True if name != 0.

Definition at line 155 of file PhyloNode.h.

References bpp::PhyloNode::name_.

Referenced by bpp::PhyloNode::getName().

◆ hasProperty()

bool bpp::PhyloNode::hasProperty ( const std::string & name ) const

inlineinherited

Definition at line 243 of file PhyloNode.h.

References bpp::PhyloNode::properties_.

Referenced by bpp::PhyloNode::deleteProperty(), bpp::PhyloNode::getProperty(), bpp::PhyloNode::removeProperty(), and bpp::PhyloNode::setProperty().

◆ isMixture()

bool bpp::ProcessComputationNode::isMixture ( ) const

inlineinherited

Definition at line 62 of file ProcessComputationTree.h.

References bpp::PhyloNode::getProperty(), bpp::ProcessComputationNode::getSpeciesIndex(), and bpp::TextTools::toString().

◆ isSpeciation()

bool bpp::ProcessComputationNode::isSpeciation ( ) const

inlineinherited

Definition at line 54 of file ProcessComputationTree.h.

References bpp::PhyloNode::getProperty(), bpp::ProcessComputationNode::getSpeciesIndex(), and bpp::TextTools::toString().

◆ removeProperties()

void bpp::PhyloNode::removeProperties ( )

inlineinherited

Remove all node properties.

Attached objects will not be deleted.

Definition at line 226 of file PhyloNode.h.

References bpp::PhyloNode::properties_.

◆ removeProperty()

Clonable* bpp::PhyloNode::removeProperty ( const std::string & name )

inlineinherited

Definition at line 198 of file PhyloNode.h.

References bpp::PhyloNode::hasProperty(), and bpp::PhyloNode::properties_.

◆ setName()

void bpp::PhyloNode::setName ( const std::string & name )

inlineinherited

Give a name or update the name associated to the node.

Parameters

name	The name to give to the node.

Definition at line 137 of file PhyloNode.h.

References bpp::PhyloNode::name_.

◆ setProperty()

void bpp::PhyloNode::setProperty	(	const std::string &	name,
		const Clonable &	property
	)

inlineinherited

Set/add a node property.

If no property with the same name is found, the new property will be added to the list. Conversely, the property will be deleted and replaced by the new one. If you want to keep a copy of the old property, consider using the removeProperty function before.

Parameters