The phylogenetic tree class. More...

#include <Bpp/Phyl/BipartitionList.h>

Inheritance diagram for bpp::TreeTemplate< N >:

Collaboration diagram for bpp::TreeTemplate< N >:

Public Member Functions
	TreeTemplate ()

	TreeTemplate (const TreeTemplate< N > &t)

	TreeTemplate (const Tree &t)

	TreeTemplate (N *root)

TreeTemplate< N > &	operator= (const TreeTemplate< N > &t)

TreeTemplate< N > *	cloneSubtree (int newRootId) const
	clones a Subtree rooted at given node Id More...

virtual	~TreeTemplate ()

TreeTemplate< N > *	clone () const

std::string	getName () const

void	setName (const std::string &name)

int	getRootId () const

size_t	getNumberOfLeaves () const

size_t	getNumberOfNodes () const

int	getLeafId (const std::string &name) const throw (NodeNotFoundException)

std::vector< int >	getLeavesId () const

std::vector< int >	getNodesId () const

std::vector< int >	getInnerNodesId () const

std::vector< int >	getBranchesId () const

std::vector< double >	getBranchLengths () const

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

std::vector< int >	getSonsId (int parentId) const throw (NodeNotFoundException)

std::vector< int >	getAncestorsId (int nodeId) const throw (NodeNotFoundException)

int	getFatherId (int parentId) const throw (NodeNotFoundException)

bool	hasFather (int nodeId) const throw (NodeNotFoundException)

std::string	getNodeName (int nodeId) const throw (NodeNotFoundException)

bool	hasNodeName (int nodeId) const throw (NodeNotFoundException)

void	setNodeName (int nodeId, const std::string &name) throw (NodeNotFoundException)

void	deleteNodeName (int nodeId) throw (NodeNotFoundException)

bool	hasNode (int nodeId) const

bool	isLeaf (int nodeId) const throw (NodeNotFoundException)

bool	isRoot (int nodeId) const throw (NodeNotFoundException)

double	getDistanceToFather (int nodeId) const

void	setDistanceToFather (int nodeId, double length)

void	deleteDistanceToFather (int nodeId)

bool	hasDistanceToFather (int nodeId) const

bool	hasNodeProperty (int nodeId, const std::string &name) const throw (NodeNotFoundException)

void	setNodeProperty (int nodeId, const std::string &name, const Clonable &property) throw (NodeNotFoundException)

Clonable *	getNodeProperty (int nodeId, const std::string &name) throw (NodeNotFoundException)

const Clonable *	getNodeProperty (int nodeId, const std::string &name) const throw (NodeNotFoundException)

Clonable *	removeNodeProperty (int nodeId, const std::string &name) throw (NodeNotFoundException)

std::vector< std::string >	getNodePropertyNames (int nodeId) const throw (NodeNotFoundException)

bool	hasBranchProperty (int nodeId, const std::string &name) const throw (NodeNotFoundException)

void	setBranchProperty (int nodeId, const std::string &name, const Clonable &property) throw (NodeNotFoundException)

Clonable *	getBranchProperty (int nodeId, const std::string &name) throw (NodeNotFoundException)

const Clonable *	getBranchProperty (int nodeId, const std::string &name) const throw (NodeNotFoundException)

Clonable *	removeBranchProperty (int nodeId, const std::string &name) throw (NodeNotFoundException)

std::vector< std::string >	getBranchPropertyNames (int nodeId) const throw (NodeNotFoundException)

void	rootAt (int nodeId) throw (NodeNotFoundException)
	Change the root node. More...

void	newOutGroup (int nodeId) throw (NodeNotFoundException)
	Root a tree by specifying an outgroup. More...

bool	isRooted () const
	Tell if the tree is rooted. More...

bool	unroot () throw (UnrootedTreeException)
	Unroot a rooted tree. More...

void	resetNodesId ()
	Number nodes. More...

bool	isMultifurcating () const
	Tell if the tree is multifurcating. More...

template<class N2 >
bool	hasSameTopologyAs (const TreeTemplate< N2 > &tree, bool ordered=false) const
	Tells if this tree has the same topology as the one given for comparison. More...

std::vector< double >	getBranchLengths () throw (NodeException)
	Get all the branch lengths of a tree. More...

double	getTotalLength () throw (NodeException)
	Get the total length (sum of all branch lengths) of a tree. More...

void	setBranchLengths (double brLen)
	Set all the branch lengths of a tree. More...

void	setVoidBranchLengths (double brLen)
	Give a length to branches that don't have one in a tree. More...

void	scaleTree (double factor) throw (NodeException)
	Scale a given tree. More...

int	getNextId ()
	Get an id. More...

void	swapNodes (int parentId, size_t i1, size_t i2) throw (NodeNotFoundException, IndexOutOfBoundsException)

Specific methods
virtual void	setRootNode (N *root)

virtual N *	getRootNode ()

virtual const N *	getRootNode () const

virtual std::vector< const N * >	getLeaves () const

virtual std::vector< N * >	getLeaves ()

virtual std::vector< const N * >	getNodes () const

virtual std::vector< N * >	getNodes ()

virtual std::vector< const N * >	getInnerNodes () const

virtual std::vector< N * >	getInnerNodes ()

virtual N *	getNode (int id, bool checkId=false) throw (NodeNotFoundException, Exception)

virtual const N *	getNode (int id, bool checkId=false) const throw (NodeNotFoundException, Exception)

virtual N *	getNode (const std::string &name) throw (NodeNotFoundException, Exception)

virtual const N *	getNode (const std::string &name) const throw (NodeNotFoundException, Exception)

void	rootAt (N *newRoot)

void	newOutGroup (N *outGroup)

Acting on topology.
void	swapNodes (const Tree &tree, int nodeId, size_t i1=0, size_t i2=1) throw (NodeNotFoundException,IndexOutOfBoundsException)
	Swap two son nodes. More...

Private Attributes
N *	root_

std::string	name_

Detailed Description

template<class N>
class bpp::TreeTemplate< N >

The phylogenetic tree class.

This class is part of the object implementation of phylogenetic trees. Tree are made made of nodes, instances of the class Node. It is possible to use a tree with more complexe Node classes, but currently all nodes of a tree have to be of the same class.

Trees are oriented (rooted), i.e. each node has one father node and possibly many son nodes. Leaves are nodes without descendant and root is defined has the without father. Inner nodes will generally contain two descendants (the tree is then called bifurcating), but mutlifurcating trees are also allowed with this kind of description. In the rooted case, each inner node also defines a subtree. This allows to work recursively on trees, which is very convenient in most cases. To deal with non-rooted trees, we place an artificial root at a particular node: hence the root node appears to be trifurcated. This is the way unrooted trees are described in the parenthetic description, the so called Newick format.

To clone a tree from from another tree with a different template, consider using the TreeTools::cloneSutree<N>() method:

Tree * t = new Tree<Node>(...)
NodeTemplate<int> * newRoot = TreeTools::cloneSubtree< NodeTemplate<int> >(* (t -> getRootNode()))
Tree< NodeTemplate<int> > * tt = new Tree< NodeTemplate<int> >(* newRoot);

The getNextId() method sends a id value which is not used in the tree. In the current implementation, it uses the TreeTools::getMPNUId() method. This avoids to use duplicated ids, but is time consuming. In most cases, it is of better efficiency if the user deal with the ids himself, by using the Node::setId() method. The TreeTools::getMaxId() method may also prove useful in this respect. The resetNodesId() method can also be used to re-initialize all ids.

See also: Node; NodeTemplate; TreeTools

Definition at line 56 of file BipartitionList.h.

Constructor & Destructor Documentation

◆ TreeTemplate() [1/4]

template<class N>

bpp::TreeTemplate< N >::TreeTemplate ( )

inline

Definition at line 105 of file TreeTemplate.h.

◆ TreeTemplate() [2/4]

template<class N>

bpp::TreeTemplate< N >::TreeTemplate ( const TreeTemplate< N > & t )

inline

Definition at line 108 of file TreeTemplate.h.

◆ TreeTemplate() [3/4]

template<class N>

bpp::TreeTemplate< N >::TreeTemplate ( const Tree & t )

inline

Definition at line 116 of file TreeTemplate.h.

◆ TreeTemplate() [4/4]

template<class N>

bpp::TreeTemplate< N >::TreeTemplate ( N * root )

inline

Definition at line 124 of file TreeTemplate.h.

◆ ~TreeTemplate()

template<class N>

virtual bpp::TreeTemplate< N >::~TreeTemplate ( )

inlinevirtual

Definition at line 145 of file TreeTemplate.h.

Member Function Documentation

◆ clone()

template<class N>

TreeTemplate<N>* bpp::TreeTemplate< N >::clone ( ) const

inlinevirtual

Implements bpp::Tree.

Definition at line 151 of file TreeTemplate.h.

Referenced by bpp::TreeTemplate< bpp::NodeTemplate >::hasSameTopologyAs().

◆ cloneSubtree()

template<class N>

TreeTemplate<N>* bpp::TreeTemplate< N >::cloneSubtree ( int newRootId ) const

inlinevirtual

clones a Subtree rooted at given node Id

Implements bpp::Tree.

Definition at line 139 of file TreeTemplate.h.

◆ deleteDistanceToFather()

template<class N>

void bpp::TreeTemplate< N >::deleteDistanceToFather ( int nodeId )

inlinevirtual

Implements bpp::Tree.

Definition at line 208 of file TreeTemplate.h.

◆ deleteNodeName()

template<class N>

void bpp::TreeTemplate< N >::deleteNodeName	(	int	nodeId	)
throw	(	NodeNotFoundException
	)

inlinevirtual

Implements bpp::Tree.

Definition at line 196 of file TreeTemplate.h.

◆ getAncestorsId()

template<class N>

std::vector<int> bpp::TreeTemplate< N >::getAncestorsId	(	int	nodeId	)	const
throw	(	NodeNotFoundException
	)

inlinevirtual

Implements bpp::Tree.

Definition at line 184 of file TreeTemplate.h.

◆ getBranchesId()

template<class N>

std::vector<int> bpp::TreeTemplate< N >::getBranchesId ( ) const

inlinevirtual

Implements bpp::Tree.

Definition at line 176 of file TreeTemplate.h.

◆ getBranchLengths() [1/2]

template<class N>

std::vector<double> bpp::TreeTemplate< N >::getBranchLengths ( ) const

inlinevirtual

Implements bpp::Tree.

Definition at line 178 of file TreeTemplate.h.

◆ getBranchLengths() [2/2]

template<class N>

std::vector<double> bpp::TreeTemplate< N >::getBranchLengths	(		)
throw	(	NodeException
	)

inlinevirtual

Get all the branch lengths of a tree.

Returns: A vector with all branch lengths.

Exceptions

NodeException If a branch length is lacking.

Implements bpp::Tree.

Definition at line 343 of file TreeTemplate.h.

◆ getBranchProperty() [1/2]

template<class N>

Clonable* bpp::TreeTemplate< N >::getBranchProperty	(	int	nodeId,
		const std::string &	name
	)
throw	(	NodeNotFoundException
	)

inlinevirtual

Implements bpp::Tree.

Definition at line 228 of file TreeTemplate.h.

Referenced by bpp::TreeTemplate< bpp::NodeTemplate >::rootAt().

◆ getBranchProperty() [2/2]

template<class N>

const Clonable* bpp::TreeTemplate< N >::getBranchProperty	(	int	nodeId,
		const std::string &	name
	)		const
throw	(	NodeNotFoundException
	)

inlinevirtual

Implements bpp::Tree.

Definition at line 230 of file TreeTemplate.h.

◆ getBranchPropertyNames()

template<class N>

std::vector<std::string> bpp::TreeTemplate< N >::getBranchPropertyNames	(	int	nodeId	)	const
throw	(	NodeNotFoundException
	)

inlinevirtual

Implements bpp::Tree.

Definition at line 234 of file TreeTemplate.h.

◆ getDistanceToFather()

template<class N>

double bpp::TreeTemplate< N >::getDistanceToFather ( int nodeId ) const

inlinevirtual

Implements bpp::Tree.

Definition at line 204 of file TreeTemplate.h.

Referenced by bpp::TreeTemplate< bpp::NodeTemplate >::rootAt().

◆ getFatherId()

template<class N>

int bpp::TreeTemplate< N >::getFatherId	(	int	parentId	)	const
throw	(	NodeNotFoundException
	)

inlinevirtual

Implements bpp::Tree.

Definition at line 186 of file TreeTemplate.h.

◆ getInnerNodes() [1/2]

template<class N>

virtual std::vector<const N*> bpp::TreeTemplate< N >::getInnerNodes ( ) const

inlinevirtual

Definition at line 415 of file TreeTemplate.h.

◆ getInnerNodes() [2/2]

template<class N>

virtual std::vector<N*> bpp::TreeTemplate< N >::getInnerNodes ( )

inlinevirtual

Definition at line 417 of file TreeTemplate.h.

◆ getInnerNodesId()

template<class N>

std::vector<int> bpp::TreeTemplate< N >::getInnerNodesId ( ) const

inlinevirtual

Implements bpp::Tree.

Definition at line 174 of file TreeTemplate.h.

◆ getLeafId()

template<class N>

int bpp::TreeTemplate< N >::getLeafId	(	const std::string &	name	)	const
throw	(	NodeNotFoundException
	)

inlinevirtual

Implements bpp::Tree.

Definition at line 168 of file TreeTemplate.h.

◆ getLeaves() [1/2]

template<class N>

virtual std::vector<const N*> bpp::TreeTemplate< N >::getLeaves ( ) const

inlinevirtual

Definition at line 407 of file TreeTemplate.h.

Referenced by bpp::NexusIOTree::read().

◆ getLeaves() [2/2]

template<class N>

virtual std::vector<N*> bpp::TreeTemplate< N >::getLeaves ( )

inlinevirtual

Definition at line 409 of file TreeTemplate.h.

◆ getLeavesId()

template<class N>

std::vector<int> bpp::TreeTemplate< N >::getLeavesId ( ) const

inlinevirtual

Implements bpp::Tree.

Definition at line 170 of file TreeTemplate.h.

◆ getLeavesNames()

template<class N>

std::vector<std::string> bpp::TreeTemplate< N >::getLeavesNames ( ) const

inlinevirtual

Implements bpp::Tree.

Definition at line 180 of file TreeTemplate.h.

Referenced by bpp::TreeTemplateTools::getDistanceMatrix().

◆ getName()

template<class N>

std::string bpp::TreeTemplate< N >::getName ( ) const

inlinevirtual

Methods:

Implements bpp::Tree.

Definition at line 158 of file TreeTemplate.h.

◆ getNextId()

template<class N>

int bpp::TreeTemplate< N >::getNextId ( )

inlinevirtual

Get an id.

Returns: an unused node id.

Implements bpp::Tree.

Definition at line 383 of file TreeTemplate.h.

Referenced by bpp::TreeTemplate< bpp::NodeTemplate >::newOutGroup().

◆ getNode() [1/4]

template<class N>

virtual N* bpp::TreeTemplate< N >::getNode	(	int	id,
		bool	checkId = `false`
	)
throw	(	NodeNotFoundException,
		Exception
	)

inlinevirtual

Definition at line 419 of file TreeTemplate.h.

◆ getNode() [2/4]

template<class N>

virtual const N* bpp::TreeTemplate< N >::getNode	(	int	id,
		bool	checkId = `false`
	)		const
throw	(	NodeNotFoundException,
		Exception
	)

inlinevirtual

Definition at line 436 of file TreeTemplate.h.

◆ getNode() [3/4]

template<class N>

virtual N* bpp::TreeTemplate< N >::getNode	(	const std::string &	name	)
throw	(	NodeNotFoundException,
		Exception
	)

inlinevirtual

Definition at line 453 of file TreeTemplate.h.

◆ getNode() [4/4]

template<class N>

virtual const N* bpp::TreeTemplate< N >::getNode	(	const std::string &	name	)	const
throw	(	NodeNotFoundException,
		Exception
	)

inlinevirtual

Definition at line 462 of file TreeTemplate.h.

◆ getNodeName()

template<class N>

std::string bpp::TreeTemplate< N >::getNodeName	(	int	nodeId	)	const
throw	(	NodeNotFoundException
	)

inlinevirtual

Implements bpp::Tree.

Definition at line 190 of file TreeTemplate.h.

◆ getNodeProperty() [1/2]

template<class N>

Clonable* bpp::TreeTemplate< N >::getNodeProperty	(	int	nodeId,
		const std::string &	name
	)
throw	(	NodeNotFoundException
	)

inlinevirtual

Implements bpp::Tree.

Definition at line 216 of file TreeTemplate.h.

◆ getNodeProperty() [2/2]

template<class N>

const Clonable* bpp::TreeTemplate< N >::getNodeProperty	(	int	nodeId,
		const std::string &	name
	)		const
throw	(	NodeNotFoundException
	)

inlinevirtual

Implements bpp::Tree.

Definition at line 218 of file TreeTemplate.h.

◆ getNodePropertyNames()

template<class N>

std::vector<std::string> bpp::TreeTemplate< N >::getNodePropertyNames	(	int	nodeId	)	const
throw	(	NodeNotFoundException
	)

inlinevirtual

Implements bpp::Tree.

Definition at line 222 of file TreeTemplate.h.

◆ getNodes() [1/2]

template<class N>

virtual std::vector<const N*> bpp::TreeTemplate< N >::getNodes ( ) const

inlinevirtual

Definition at line 411 of file TreeTemplate.h.

Referenced by bpp::RewardMappingTools::computeRewardVectors(), bpp::SubstitutionMappingTools::computeSubstitutionVectors(), bpp::SubstitutionMappingTools::computeSubstitutionVectorsMarginal(), bpp::SubstitutionMappingTools::computeSubstitutionVectorsNoAveraging(), bpp::SubstitutionMappingTools::computeSubstitutionVectorsNoAveragingMarginal(), bpp::TreeTemplate< bpp::NodeTemplate >::resetNodesId(), bpp::NNITopologySearch::searchBetter(), bpp::NNITopologySearch::searchFast(), and bpp::NNITopologySearch::searchPhyML().

◆ getNodes() [2/2]

template<class N>

virtual std::vector<N*> bpp::TreeTemplate< N >::getNodes ( )

inlinevirtual

Definition at line 413 of file TreeTemplate.h.

◆ getNodesId()

template<class N>

std::vector<int> bpp::TreeTemplate< N >::getNodesId ( ) const

inlinevirtual

Implements bpp::Tree.

Definition at line 172 of file TreeTemplate.h.

◆ getNumberOfLeaves()

template<class N>

size_t bpp::TreeTemplate< N >::getNumberOfLeaves ( ) const

inlinevirtual

Implements bpp::Tree.

Definition at line 164 of file TreeTemplate.h.

◆ getNumberOfNodes()

template<class N>

size_t bpp::TreeTemplate< N >::getNumberOfNodes ( ) const

inlinevirtual

Implements bpp::Tree.

Definition at line 166 of file TreeTemplate.h.

◆ getRootId()

template<class N>

int bpp::TreeTemplate< N >::getRootId ( ) const

inlinevirtual

Implements bpp::Tree.

Definition at line 162 of file TreeTemplate.h.

Referenced by bpp::TreeTemplateTools::midRoot(), and bpp::TreeTemplate< bpp::NodeTemplate >::newOutGroup().

◆ getRootNode() [1/2]

template<class N>

virtual N* bpp::TreeTemplate< N >::getRootNode ( )

inlinevirtual

Definition at line 403 of file TreeTemplate.h.

Referenced by bpp::BipartitionList::BipartitionList(), bpp::TreeTemplateTools::getDistanceMatrix(), bpp::TreeTemplateTools::getRadius(), bpp::AbstractNonHomogeneousTreeLikelihood::init_(), bpp::TreeTemplateTools::midRoot(), bpp::PhyloStatistics::setTree(), bpp::Nhx::treeToParenthesis(), and bpp::TreeTemplateTools::treeToParenthesis().

◆ getRootNode() [2/2]

template<class N>

virtual const N* bpp::TreeTemplate< N >::getRootNode ( ) const

inlinevirtual

Definition at line 405 of file TreeTemplate.h.

◆ getSonsId()

template<class N>

std::vector<int> bpp::TreeTemplate< N >::getSonsId	(	int	parentId	)	const
throw	(	NodeNotFoundException
	)

inlinevirtual

Implements bpp::Tree.

Definition at line 182 of file TreeTemplate.h.

◆ getTotalLength()

template<class N>

double bpp::TreeTemplate< N >::getTotalLength	(		)
throw	(	NodeException
	)

inlinevirtual

Get the total length (sum of all branch lengths) of a tree.

Returns: The total length of the subtree.

Exceptions

NodeException If a branch length is lacking.

Implements bpp::Tree.

Definition at line 354 of file TreeTemplate.h.

◆ hasBranchProperty()

template<class N>

bool bpp::TreeTemplate< N >::hasBranchProperty	(	int	nodeId,
		const std::string &	name
	)		const
throw	(	NodeNotFoundException
	)

inlinevirtual

Implements bpp::Tree.

Definition at line 224 of file TreeTemplate.h.

◆ hasDistanceToFather()

template<class N>

bool bpp::TreeTemplate< N >::hasDistanceToFather ( int nodeId ) const

inlinevirtual

Implements bpp::Tree.

Definition at line 210 of file TreeTemplate.h.

Referenced by bpp::TreeTemplate< bpp::NodeTemplate >::rootAt().

◆ hasFather()

template<class N>

bool bpp::TreeTemplate< N >::hasFather	(	int	nodeId	)	const
throw	(	NodeNotFoundException
	)

inlinevirtual

Implements bpp::Tree.

Definition at line 188 of file TreeTemplate.h.

◆ hasNode()

template<class N>

bool bpp::TreeTemplate< N >::hasNode ( int nodeId ) const

inlinevirtual

Implements bpp::Tree.

Definition at line 198 of file TreeTemplate.h.

◆ hasNodeName()

template<class N>

bool bpp::TreeTemplate< N >::hasNodeName	(	int	nodeId	)	const
throw	(	NodeNotFoundException
	)

inlinevirtual

Implements bpp::Tree.

Definition at line 192 of file TreeTemplate.h.

◆ hasNodeProperty()

template<class N>

bool bpp::TreeTemplate< N >::hasNodeProperty	(	int	nodeId,
		const std::string &	name
	)		const
throw	(	NodeNotFoundException
	)

inlinevirtual

Implements bpp::Tree.

Definition at line 212 of file TreeTemplate.h.

◆ hasSameTopologyAs()

template<class N>

template<class N2 >

bool bpp::TreeTemplate< N >::hasSameTopologyAs	(	const TreeTemplate< N2 > &	tree,
		bool	ordered = `false`
	)		const

inline

Tells if this tree has the same topology as the one given for comparison.

This method compares recursively all subtrees. The comparison is performed only on the nodes names and the parental relationships. Nodes ids are ignored, and so are branch lengths and any branch/node properties. The default is to ignore the ordering of the descendants, that is (A,B),C) will be considered as having the same topology as (B,A),C). Multifurcations are permited. If ordering is ignored, a copy of the two trees to be compared is performed and are ordered before comparison, making the whole comparison slower and more memory greedy.

Parameters

tree	The tree to be compared with.
ordered	Should the ordering of the branching be taken into account?

Returns: True if the input tree has the same topology as this one.

Definition at line 316 of file TreeTemplate.h.

◆ isLeaf()

template<class N>

bool bpp::TreeTemplate< N >::isLeaf	(	int	nodeId	)	const
throw	(	NodeNotFoundException
	)

inlinevirtual

Implements bpp::Tree.

Definition at line 200 of file TreeTemplate.h.

◆ isMultifurcating()

template<class N>

bool bpp::TreeTemplate< N >::isMultifurcating ( ) const

inlinevirtual

Tell if the tree is multifurcating.

Returns: True if the tree is multifurcating.

Implements bpp::Tree.

Definition at line 293 of file TreeTemplate.h.

◆ isRoot()

template<class N>

bool bpp::TreeTemplate< N >::isRoot	(	int	nodeId	)	const
throw	(	NodeNotFoundException
	)

inlinevirtual

Implements bpp::Tree.

Definition at line 202 of file TreeTemplate.h.

◆ isRooted()

template<class N>

bool bpp::TreeTemplate< N >::isRooted ( ) const

inlinevirtual

Tell if the tree is rooted.

Returns: True if the tree is rooted.

Implements bpp::Tree.

Definition at line 240 of file TreeTemplate.h.

Referenced by bpp::TreeTemplateTools::midRoot(), bpp::TreeTemplate< bpp::NodeTemplate >::newOutGroup(), bpp::TreeTemplate< bpp::NodeTemplate >::rootAt(), and bpp::TreeTemplate< bpp::NodeTemplate >::unroot().

◆ newOutGroup() [1/2]

template<class N>

void bpp::TreeTemplate< N >::newOutGroup	(	int	nodeId	)
throw	(	NodeNotFoundException
	)

inlinevirtual

Root a tree by specifying an outgroup.

If the tree is rooted, unroot it first, change the root node and then reroot the tree using the previous root id. If the tree is unrooted, change the root node and then create a new root node.

Parameters

nodeId The id of the node that will be the new root.

Implements bpp::Tree.

Definition at line 238 of file TreeTemplate.h.

Referenced by bpp::TreeTemplate< bpp::NodeTemplate >::newOutGroup().

◆ newOutGroup() [2/2]

template<class N>

void bpp::TreeTemplate< N >::newOutGroup ( N * outGroup )

inline

Definition at line 503 of file TreeTemplate.h.

◆ operator=()

template<class N>

TreeTemplate<N>& bpp::TreeTemplate< N >::operator= ( const TreeTemplate< N > & t )

inline

Definition at line 130 of file TreeTemplate.h.

◆ removeBranchProperty()

template<class N>

Clonable* bpp::TreeTemplate< N >::removeBranchProperty	(	int	nodeId,
		const std::string &	name
	)
throw	(	NodeNotFoundException
	)

inlinevirtual

Implements bpp::Tree.

Definition at line 232 of file TreeTemplate.h.

◆ removeNodeProperty()

template<class N>

Clonable* bpp::TreeTemplate< N >::removeNodeProperty	(	int	nodeId,
		const std::string &	name
	)
throw	(	NodeNotFoundException
	)

inlinevirtual

Implements bpp::Tree.

Definition at line 220 of file TreeTemplate.h.

◆ resetNodesId()

template<class N>

void bpp::TreeTemplate< N >::resetNodesId ( )

inlinevirtual

Number nodes.

Implements bpp::Tree.

Definition at line 284 of file TreeTemplate.h.

Referenced by bpp::TreeTemplateTools::getRandomTree(), bpp::Nhx::parenthesisToTree(), bpp::TreeTemplateTools::parenthesisToTree(), and bpp::BipartitionList::toTree().

◆ rootAt() [1/2]

template<class N>

void bpp::TreeTemplate< N >::rootAt	(	int	nodeId	)
throw	(	NodeNotFoundException
	)

inlinevirtual

Change the root node.

Works on unrooted tree. If the tree is rooted, the method unroots it first.

Parameters

nodeId The id of the node that will be the new root.

Implements bpp::Tree.

Definition at line 236 of file TreeTemplate.h.

Referenced by bpp::TreeTemplateTools::getBestRootInSubtree_(), bpp::TreeTemplateTools::midRoot(), bpp::TreeTemplate< bpp::NodeTemplate >::newOutGroup(), and bpp::TreeTemplate< bpp::NodeTemplate >::rootAt().

◆ rootAt() [2/2]

template<class N>

void bpp::TreeTemplate< N >::rootAt ( N * newRoot )

inline

Definition at line 471 of file TreeTemplate.h.

◆ scaleTree()

template<class N>

void bpp::TreeTemplate< N >::scaleTree	(	double	factor	)
throw	(	NodeException
	)

inlinevirtual

Scale a given tree.

Multiply all branch lengths by a given factor.

Parameters

factor The factor to multiply all branch lengths with.

Exceptions

NodeException If a branch length is lacking.

Implements bpp::Tree.

Definition at line 375 of file TreeTemplate.h.

◆ setBranchLengths()

template<class N>

void bpp::TreeTemplate< N >::setBranchLengths ( double brLen )

inlinevirtual

Set all the branch lengths of a tree.

Parameters

brLen The branch length to apply.

Implements bpp::Tree.

Definition at line 359 of file TreeTemplate.h.

◆ setBranchProperty()

template<class N>

void bpp::TreeTemplate< N >::setBranchProperty	(	int	nodeId,
		const std::string &	name,
		const Clonable &	property
	)
throw	(	NodeNotFoundException
	)

inlinevirtual

Implements bpp::Tree.

Definition at line 226 of file TreeTemplate.h.

◆ setDistanceToFather()

template<class N>

void bpp::TreeTemplate< N >::setDistanceToFather	(	int	nodeId,
		double	length
	)

inlinevirtual

Implements bpp::Tree.

Definition at line 206 of file TreeTemplate.h.

◆ setName()

template<class N>

void bpp::TreeTemplate< N >::setName ( const std::string & name )

inlinevirtual

Implements bpp::Tree.

Definition at line 160 of file TreeTemplate.h.

◆ setNodeName()

template<class N>

void bpp::TreeTemplate< N >::setNodeName	(	int	nodeId,
		const std::string &	name
	)
throw	(	NodeNotFoundException
	)

inlinevirtual

Implements bpp::Tree.

Definition at line 194 of file TreeTemplate.h.

◆ setNodeProperty()

template<class N>

void bpp::TreeTemplate< N >::setNodeProperty	(	int	nodeId,
		const std::string &	name,
		const Clonable &	property
	)
throw	(	NodeNotFoundException
	)

inlinevirtual

Implements bpp::Tree.

Definition at line 214 of file TreeTemplate.h.

◆ setRootNode()

template<class N>

virtual void bpp::TreeTemplate< N >::setRootNode ( N * root )

inlinevirtual

Definition at line 401 of file TreeTemplate.h.

Referenced by bpp::Nhx::parenthesisToTree(), bpp::TreeTemplateTools::parenthesisToTree(), and bpp::TreeTemplate< bpp::NodeTemplate >::unroot().

◆ setVoidBranchLengths()

template<class N>

void bpp::TreeTemplate< N >::setVoidBranchLengths ( double brLen )

inlinevirtual

Give a length to branches that don't have one in a tree.

Parameters

brLen The branch length to apply.

Implements bpp::Tree.

Definition at line 367 of file TreeTemplate.h.

◆ swapNodes() [1/2]

void bpp::Tree::swapNodes	(	const Tree &	tree,
		int	nodeId,
		size_t	i1 = `0`,
		size_t	i2 = `1`
	)
throw	(	NodeNotFoundException,
		IndexOutOfBoundsException
	)

inherited

Swap two son nodes.

Parameters

tree	The tree.
nodeId	The node.
i1	First son node index.
i2	Second son node index.

Exceptions

NodeNotFoundException	If the node is not found.
IndexOutOfBoundsException	If one node index is not valid, or if the node

◆ swapNodes() [2/2]

template<class N>

void bpp::TreeTemplate< N >::swapNodes	(	int	parentId,
		size_t	i1,
		size_t	i2
	)
throw	(	NodeNotFoundException,
		IndexOutOfBoundsException
	)

inline

Definition at line 388 of file TreeTemplate.h.

◆ unroot()

template<class N>

bool bpp::TreeTemplate< N >::unroot	(		)
throw	(	UnrootedTreeException
	)

inlinevirtual

Unroot a rooted tree.

Returns: True if the tree has been unrooted.

Exceptions

UnrootedTreeException If the tree is already rooted.

Implements bpp::Tree.

Definition at line 242 of file TreeTemplate.h.

Referenced by bpp::TreeTemplateTools::midRoot(), bpp::TreeTemplate< bpp::NodeTemplate >::newOutGroup(), and bpp::TreeTemplate< bpp::NodeTemplate >::rootAt().

Member Data Documentation

◆ name_

template<class N>

std::string bpp::TreeTemplate< N >::name_

private

Definition at line 101 of file TreeTemplate.h.

Referenced by bpp::TreeTemplate< bpp::NodeTemplate >::getName(), bpp::TreeTemplate< bpp::NodeTemplate >::operator=(), and bpp::TreeTemplate< bpp::NodeTemplate >::setName().

◆ root_

template<class N>

N* bpp::TreeTemplate< N >::root_

private

Fields:

Definition at line 100 of file TreeTemplate.h.

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

Bpp/Phyl/BipartitionList.h
Bpp/Phyl/TreeTemplate.h

Public Member Functions

Private Attributes

Detailed Description

template<class N> class bpp::TreeTemplate< N >

Constructor & Destructor Documentation

◆ TreeTemplate() [1/4]

◆ TreeTemplate() [2/4]

◆ TreeTemplate() [3/4]

◆ TreeTemplate() [4/4]

◆ ~TreeTemplate()

Member Function Documentation

◆ clone()

◆ cloneSubtree()

◆ deleteDistanceToFather()

◆ deleteNodeName()

◆ getAncestorsId()

◆ getBranchesId()

◆ getBranchLengths() [1/2]

◆ getBranchLengths() [2/2]

◆ getBranchProperty() [1/2]

◆ getBranchProperty() [2/2]

◆ getBranchPropertyNames()

◆ getDistanceToFather()

◆ getFatherId()

◆ getInnerNodes() [1/2]

◆ getInnerNodes() [2/2]

◆ getInnerNodesId()

◆ getLeafId()

◆ getLeaves() [1/2]

◆ getLeaves() [2/2]

◆ getLeavesId()

◆ getLeavesNames()

◆ getName()

◆ getNextId()

◆ getNode() [1/4]

◆ getNode() [2/4]

◆ getNode() [3/4]

◆ getNode() [4/4]

◆ getNodeName()

◆ getNodeProperty() [1/2]

◆ getNodeProperty() [2/2]

◆ getNodePropertyNames()

◆ getNodes() [1/2]

◆ getNodes() [2/2]

◆ getNodesId()

◆ getNumberOfLeaves()

◆ getNumberOfNodes()

◆ getRootId()

◆ getRootNode() [1/2]

◆ getRootNode() [2/2]

◆ getSonsId()

◆ getTotalLength()

◆ hasBranchProperty()

◆ hasDistanceToFather()

◆ hasFather()

◆ hasNode()

◆ hasNodeName()

◆ hasNodeProperty()

◆ hasSameTopologyAs()

◆ isLeaf()

◆ isMultifurcating()

◆ isRoot()

◆ isRooted()

◆ newOutGroup() [1/2]

◆ newOutGroup() [2/2]

◆ operator=()

◆ removeBranchProperty()

◆ removeNodeProperty()

◆ resetNodesId()

◆ rootAt() [1/2]

◆ rootAt() [2/2]

◆ scaleTree()

◆ setBranchLengths()

◆ setBranchProperty()

◆ setDistanceToFather()

◆ setName()

◆ setNodeName()

◆ setNodeProperty()

◆ setRootNode()

◆ setVoidBranchLengths()

template<class N>
class bpp::TreeTemplate< N >