A node class aware of its neighbours. More...

#include <Bpp/Phyl/Legacy/Tree/AwareNode.h>

Collaboration diagram for bpp::AwareNode:

Public Member Functions
	AwareNode ()
	Build a new void Node object. More...

	AwareNode (unsigned int id)
	Build a new Node with specified id. More...

	AwareNode (const AwareNode &node)
	Copy constructor. More...

AwareNode &	operator= (const AwareNode &node)
	Assignation operator. More...

AwareNode *	clone () const

virtual	~AwareNode ()

template<class N , class E , class I >
void	updateTree (AssociationTreeGraphImplObserver< N, E, I > *tree, unsigned int index)
	update information from TreeObserver More...

virtual bool	hasNoSon () const

Identity
virtual unsigned int	getId () const
	Get the node's id. More...

virtual void	setId (unsigned int id)
	Set this node's id. More...

virtual std::vector< unsigned int >	getSonsId () const

Distances:
virtual double	getDistanceToFather () const
	Get the distance to the father node is there is one, otherwise throw a NodeException. More...

virtual void	setDistanceToFather (double distance)
	Set or update the distance toward the father node. More...

Father:
virtual const AwareNode *	getFather () const
	Get the father of this node is there is one. More...

virtual AwareNode *	getFather ()
	Get the father of this node is there is one. More...

virtual void	setFather (AwareNode *node)
	Set the father node of this node. More...

virtual void	removeFather ()
	Remove the father of this node. More...

virtual bool	hasFather () const
	Tell if this node has a father node. More...

Sons:
virtual size_t	getNumberOfSons () const

bool	isLeaf () const

virtual std::vector< AwareNode * > &	getSons ()

virtual const AwareNode *	getSon (size_t pos) const

virtual AwareNode *	getSon (size_t pos)

virtual void	addSon (size_t pos, AwareNode *node)

virtual void	addSon (AwareNode *node)

virtual void	setSon (size_t pos, AwareNode *node)

virtual void	removeSon (size_t pos)

virtual void	removeSon (AwareNode *node)

virtual void	removeSons ()

virtual void	swap (size_t branch1, size_t branch2)

virtual size_t	getSonPosition (const AwareNode *son) const

Operators:
a positive value send the corresponding son; a negative value send the father.
AwareNode *	operator[] (int i)

const AwareNode *	operator[] (int i) const

Protected Attributes
unsigned int	id_

std::vector< AwareNode * >	sons_

AwareNode *	father_

double	distanceToFather_

Detailed Description

A node class aware of its neighbours.

This class is made the more general as possible, while keeping it very simple. It contains:

An identity tag, to identity it in the tree;
A pointer toward the father node;
A std::vector of pointer toward son nodes;
The distance from the father node:

See also: PhyloTree

Definition at line 41 of file AwareNode.h.

Constructor & Destructor Documentation

◆ AwareNode() [1/3]

bpp::AwareNode::AwareNode ( )

inline

Build a new void Node object.

Definition at line 54 of file AwareNode.h.

Referenced by clone().

◆ AwareNode() [2/3]

bpp::AwareNode::AwareNode ( unsigned int id )

inline

Build a new Node with specified id.

Definition at line 64 of file AwareNode.h.

◆ AwareNode() [3/3]

AwareNode::AwareNode ( const AwareNode & node )

Copy constructor.

Warning: THIS OPERATOR COPIES ALL FIELDS, EXCEPTED FATHER AND SON NODE POINTERS.

Need the call of updateTree after whole Tree is built.

Parameters

node	The node to copy.

Copy constructor:

Definition at line 15 of file AwareNode.cpp.

◆ ~AwareNode()

virtual bpp::AwareNode::~AwareNode ( )

inlinevirtual

Definition at line 98 of file AwareNode.h.

Member Function Documentation

◆ addSon() [1/2]

virtual void bpp::AwareNode::addSon ( AwareNode * node )

inlinevirtual

Definition at line 261 of file AwareNode.h.

References sons_.

◆ addSon() [2/2]

virtual void bpp::AwareNode::addSon	(	size_t	pos,
		AwareNode *	node
	)

inlinevirtual

Definition at line 251 of file AwareNode.h.

References sons_.

Referenced by swap().

◆ clone()

AwareNode* bpp::AwareNode::clone ( ) const

inline

Definition at line 96 of file AwareNode.h.

References AwareNode().

◆ getDistanceToFather()

virtual double bpp::AwareNode::getDistanceToFather ( ) const

inlinevirtual

Get the distance to the father node is there is one, otherwise throw a NodeException.

Returns: The distance to the father node.

Definition at line 154 of file AwareNode.h.

References distanceToFather_.

◆ getFather() [1/2]

virtual AwareNode* bpp::AwareNode::getFather ( )

inlinevirtual

Get the father of this node is there is one.

Returns: A pointer toward the father node, 0 if there is not.

Definition at line 193 of file AwareNode.h.

References father_.

◆ getFather() [2/2]

virtual const AwareNode* bpp::AwareNode::getFather ( ) const

inlinevirtual

Get the father of this node is there is one.

Returns: A pointer toward the father node, 0 if there is not.

Definition at line 186 of file AwareNode.h.

References father_.

◆ getId()

virtual unsigned int bpp::AwareNode::getId ( ) const

inlinevirtual

Get the node's id.

Returns: The identity tag of this node.

Definition at line 121 of file AwareNode.h.

References id_.

Referenced by getSonPosition(), and removeSon().

◆ getNumberOfSons()

virtual size_t bpp::AwareNode::getNumberOfSons ( ) const

inlinevirtual

Definition at line 227 of file AwareNode.h.

References sons_.

Referenced by hasNoSon(), and isLeaf().

◆ getSon() [1/2]

virtual AwareNode* bpp::AwareNode::getSon ( size_t pos )

inlinevirtual

Definition at line 245 of file AwareNode.h.

References sons_.

◆ getSon() [2/2]

virtual const AwareNode* bpp::AwareNode::getSon ( size_t pos ) const

inlinevirtual

Definition at line 239 of file AwareNode.h.

References sons_.

Referenced by swap().

◆ getSonPosition()

size_t AwareNode::getSonPosition ( const AwareNode * son ) const

virtual

Definition at line 51 of file AwareNode.cpp.

References getId(), sons_, and bpp::TextTools::toString().

◆ getSons()

virtual std::vector<AwareNode*>& bpp::AwareNode::getSons ( )

inlinevirtual

Definition at line 234 of file AwareNode.h.

References sons_.

◆ getSonsId()

virtual std::vector<unsigned int> bpp::AwareNode::getSonsId ( ) const

inlinevirtual

Definition at line 130 of file AwareNode.h.

References sons_.

◆ hasFather()

virtual bool bpp::AwareNode::hasFather ( ) const

inlinevirtual

Tell if this node has a father node.

Definition at line 218 of file AwareNode.h.

References father_.

◆ hasNoSon()

virtual bool bpp::AwareNode::hasNoSon ( ) const

inlinevirtual

Definition at line 331 of file AwareNode.h.

References getNumberOfSons().

◆ isLeaf()

bool bpp::AwareNode::isLeaf ( ) const

inline

Definition at line 229 of file AwareNode.h.

References getNumberOfSons().

◆ operator=()

AwareNode & AwareNode::operator= ( const AwareNode & node )

Assignation operator.

Warning: THIS OPERATOR COPIES ALL FIELDS, EXCEPTED FATHER AND SON NODE POINTERS.

Need the call of updateTree after whole Tree is built.

Parameters

node	the node to copy.

Returns: A reference toward this node.

Assignation operator:

Definition at line 23 of file AwareNode.cpp.

References distanceToFather_, father_, id_, and sons_.

◆ operator[]() [1/2]

AwareNode* bpp::AwareNode::operator[] ( int i )

inline

Definition at line 325 of file AwareNode.h.

References father_, and sons_.

◆ operator[]() [2/2]

const AwareNode* bpp::AwareNode::operator[] ( int i ) const

inline

Definition at line 327 of file AwareNode.h.

References father_, and sons_.

◆ removeFather()

virtual void bpp::AwareNode::removeFather ( )

inlinevirtual

Remove the father of this node.

Definition at line 210 of file AwareNode.h.

References father_.

◆ removeSon() [1/2]

virtual void bpp::AwareNode::removeSon ( AwareNode * node )

inlinevirtual

Definition at line 291 of file AwareNode.h.

References getId(), sons_, and bpp::TextTools::toString().

◆ removeSon() [2/2]

virtual void bpp::AwareNode::removeSon ( size_t pos )

inlinevirtual

Definition at line 284 of file AwareNode.h.

References sons_.

Referenced by swap().

◆ removeSons()

virtual void bpp::AwareNode::removeSons ( )

inlinevirtual

Definition at line 306 of file AwareNode.h.

References sons_.

◆ setDistanceToFather()

virtual void bpp::AwareNode::setDistanceToFather ( double distance )

inlinevirtual

Set or update the distance toward the father node.

Warning: a distance to the father node may be set even if no father node is specified. This is used by several tree reconstruction methods. It may also be useful for manipulating subtrees.

Parameters

distance The new distance to the father node.

Definition at line 168 of file AwareNode.h.

References distanceToFather_.

◆ setFather()

virtual void bpp::AwareNode::setFather ( AwareNode * node )

inlinevirtual

Set the father node of this node.

Parameters

node	The father node.

Definition at line 202 of file AwareNode.h.

References father_.

◆ setId()

virtual void bpp::AwareNode::setId ( unsigned int id )

inlinevirtual

Set this node's id.

Parameters

id	The new identity tag.

Definition at line 128 of file AwareNode.h.

References id_.

◆ setSon()

virtual void bpp::AwareNode::setSon	(	size_t	pos,
		AwareNode *	node
	)

inlinevirtual

Definition at line 271 of file AwareNode.h.

References sons_.

◆ swap()

void AwareNode::swap	(	size_t	branch1,
		size_t	branch2
	)

virtual

Sons:

Definition at line 35 of file AwareNode.cpp.

References addSon(), getSon(), and removeSon().

◆ updateTree()

template<class N , class E , class I >

void bpp::AwareNode::updateTree	(	AssociationTreeGraphImplObserver< N, E, I > *	tree,
		unsigned int	index
	)

update information from TreeObserver

Definition at line 335 of file AwareNode.h.

References father_, bpp::AssociationTreeGraphImplObserver< class, class, class >::getFatherOfNode(), bpp::AssociationTreeGraphImplObserver< class, class, class >::getNode(), bpp::AssociationTreeGraphImplObserver< class, class, class >::getSons(), bpp::AssociationTreeGraphImplObserver< class, class, class >::hasFather(), id_, and sons_.

Member Data Documentation

◆ distanceToFather_

double bpp::AwareNode::distanceToFather_

protected

Definition at line 48 of file AwareNode.h.

Referenced by getDistanceToFather(), operator=(), and setDistanceToFather().

◆ father_

AwareNode* bpp::AwareNode::father_

protected

Definition at line 47 of file AwareNode.h.

Referenced by getFather(), hasFather(), operator=(), operator[](), removeFather(), setFather(), and updateTree().

◆ id_

unsigned int bpp::AwareNode::id_

protected

Definition at line 45 of file AwareNode.h.

Referenced by getId(), operator=(), setId(), and updateTree().

◆ sons_

std::vector<AwareNode* > bpp::AwareNode::sons_

protected

Definition at line 46 of file AwareNode.h.

Referenced by addSon(), getNumberOfSons(), getSon(), getSonPosition(), getSons(), getSonsId(), operator=(), operator[](), removeSon(), removeSons(), setSon(), and updateTree().

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

Bpp/Phyl/Legacy/Tree/AwareNode.h
Bpp/Phyl/Legacy/Tree/AwareNode.cpp

Public Member Functions

Protected Attributes

Detailed Description

Constructor & Destructor Documentation

◆ AwareNode() [1/3]

◆ AwareNode() [2/3]

◆ AwareNode() [3/3]

◆ ~AwareNode()

Member Function Documentation

◆ addSon() [1/2]

◆ addSon() [2/2]

◆ clone()

◆ getDistanceToFather()

◆ getFather() [1/2]

◆ getFather() [2/2]

◆ getId()

◆ getNumberOfSons()

◆ getSon() [1/2]

◆ getSon() [2/2]

◆ getSonPosition()

◆ getSons()

◆ getSonsId()

◆ hasFather()

◆ hasNoSon()

◆ isLeaf()

◆ operator=()

◆ operator[]() [1/2]

◆ operator[]() [2/2]

◆ removeFather()

◆ removeSon() [1/2]

◆ removeSon() [2/2]

◆ removeSons()

◆ setDistanceToFather()

◆ setFather()

◆ setId()

◆ setSon()

◆ swap()

◆ updateTree()

Member Data Documentation

◆ distanceToFather_

◆ father_

◆ id_

◆ sons_