Tree Organization of Computing Nodes. More...

#include <Bpp/Phyl/Likelihood/ProcessComputationTree.h>

Inheritance diagram for bpp::ProcessComputationNode:

Collaboration diagram for bpp::ProcessComputationNode:

Public Member Functions
	ProcessComputationNode (const PhyloNode &node, uint speciesIndex)
	Build from a node in the phylo tree, with a specific speciesIndex (because indexes are not the same as in the ParametrizablePhyloTree. More...

	ProcessComputationNode (const ProcessComputationNode &node)

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

std::string	name_

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

Detailed Description

Tree Organization of Computing Nodes.

Stores computation tools for all nodes, for all classes.

This object has the parameters of the Tree and the rates distribution, since it manages the SpeciationComputingNodes.

Definition at line 27 of file ProcessComputationTree.h.

Constructor & Destructor Documentation

◆ ProcessComputationNode() [1/2]

bpp::ProcessComputationNode::ProcessComputationNode	(	const PhyloNode &	node,
		uint	speciesIndex
	)

inline

Build from a node in the phylo tree, with a specific speciesIndex (because indexes are not the same as in the ParametrizablePhyloTree.

Definition at line 41 of file ProcessComputationTree.h.

◆ ProcessComputationNode() [2/2]

bpp::ProcessComputationNode::ProcessComputationNode ( const ProcessComputationNode & node )

inline

Definition at line 45 of file ProcessComputationTree.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(), isMixture(), and 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

inline

Definition at line 49 of file ProcessComputationTree.h.

References speciesIndex_.

Referenced by isMixture(), and 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

inline

Definition at line 62 of file ProcessComputationTree.h.

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

◆ isSpeciation()

bool bpp::ProcessComputationNode::isSpeciation ( ) const

inline

Definition at line 54 of file ProcessComputationTree.h.

References bpp::PhyloNode::getProperty(), 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

name	The name of the property to set.
property	The property object (will be cloned).

Definition at line 175 of file PhyloNode.h.

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

Referenced by bpp::StochasticMapping::setNodeState().

Member Data Documentation

◆ name_

std::string bpp::PhyloNode::name_

privateinherited

Definition at line 62 of file PhyloNode.h.

Referenced by bpp::PhyloNode::deleteName(), bpp::PhyloNode::getName(), bpp::PhyloNode::hasName(), bpp::PhyloNode::operator=(), and bpp::PhyloNode::setName().

◆ properties_

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

mutableprivateinherited

Definition at line 65 of file PhyloNode.h.

Referenced by bpp::PhyloNode::deleteProperties(), bpp::PhyloNode::deleteProperty(), bpp::PhyloNode::getProperty(), bpp::PhyloNode::getPropertyNames(), bpp::PhyloNode::hasProperty(), bpp::PhyloNode::operator=(), bpp::PhyloNode::PhyloNode(), bpp::PhyloNode::removeProperties(), bpp::PhyloNode::removeProperty(), and bpp::PhyloNode::setProperty().

◆ speciesIndex_

const uint bpp::ProcessComputationNode::speciesIndex_

private

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

Definition at line 33 of file ProcessComputationTree.h.

Referenced by getSpeciesIndex().

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

Bpp/Phyl/Likelihood/ProcessComputationTree.h

Public Member Functions

Private Attributes

Detailed Description

Constructor & Destructor Documentation

◆ ProcessComputationNode() [1/2]

◆ ProcessComputationNode() [2/2]

Member Function Documentation

◆ clone()

◆ deleteName()

◆ deleteProperties()

◆ deleteProperty()

◆ getName()

◆ getProperty() [1/2]

◆ getProperty() [2/2]

◆ getPropertyNames()

◆ getSpeciesIndex()

◆ hasName()

◆ hasProperty()

◆ isMixture()

◆ isSpeciation()

◆ removeProperties()

◆ removeProperty()

◆ setName()

◆ setProperty()

Member Data Documentation

◆ name_

◆ properties_

◆ speciesIndex_