bpp::TreeTemplate< N > Class Template Reference

The phylogenetic tree class. More...

#include <Bpp/Phyl/Tree/TreeTemplate.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
size_t	getNumberOfBranches () const
int	getLeafId (const std::string &name) const
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
std::vector< int >	getAncestorsId (int nodeId) const
int	getFatherId (int parentId) const
bool	hasFather (int nodeId) const
std::string	getNodeName (int nodeId) const
bool	hasNodeName (int nodeId) const
void	setNodeName (int nodeId, const std::string &name)
void	deleteNodeName (int nodeId)
bool	hasNode (int nodeId) const
bool	isLeaf (int nodeId) const
bool	hasNoSon (int nodeId) const
bool	isRoot (int nodeId) const
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
void	setNodeProperty (int nodeId, const std::string &name, const Clonable &property)
Clonable *	getNodeProperty (int nodeId, const std::string &name)
const Clonable *	getNodeProperty (int nodeId, const std::string &name) const
Clonable *	removeNodeProperty (int nodeId, const std::string &name)
std::vector< std::string >	getNodePropertyNames (int nodeId) const
bool	hasBranchProperty (int nodeId, const std::string &name) const
void	setBranchProperty (int nodeId, const std::string &name, const Clonable &property)
Clonable *	getBranchProperty (int nodeId, const std::string &name)
const Clonable *	getBranchProperty (int nodeId, const std::string &name) const
Clonable *	removeBranchProperty (int nodeId, const std::string &name)
std::vector< std::string >	getBranchPropertyNames (int nodeId) const
void	rootAt (int nodeId)
	Change the root node. More...
void	newOutGroup (int nodeId)
	Root a tree by specifying an outgroup. More...
bool	isRooted () const
	Tell if the tree is rooted. More...
bool	unroot ()
	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 ()
	Get all the branch lengths of a tree. More...
double	getTotalLength ()
	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)
	Scale a given tree. More...
int	getNextId ()
	Get an id. More...
void	swapNodes (int parentId, size_t i1, size_t i2)
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)
virtual const N *	getNode (int id, bool checkId=false) const
virtual N *	getNode (const std::string &name)
virtual const N *	getNode (const std::string &name) const
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)
	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 57 of file TreeTemplate.h.

Constructor & Destructor Documentation

TreeTemplate() [1/4]

template<class N >

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

inline

Definition at line 70 of file TreeTemplate.h.

TreeTemplate() [2/4]

template<class N >

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

inline

Definition at line 73 of file TreeTemplate.h.

References bpp::TreeTemplate< N >::getRootNode(), and bpp::TreeTemplate< N >::root_.

TreeTemplate() [3/4]

template<class N >

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

inline

Definition at line 81 of file TreeTemplate.h.

References bpp::Tree::getRootId(), and bpp::TreeTemplate< N >::root_.

TreeTemplate() [4/4]

template<class N >

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

inline

Definition at line 89 of file TreeTemplate.h.

References bpp::TreeTemplate< N >::root_.

~TreeTemplate()

template<class N >

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

inlinevirtual

Definition at line 110 of file TreeTemplate.h.

References bpp::TreeTemplateTools::deleteSubtree(), and bpp::TreeTemplate< N >::root_.

Member Function Documentation

clone()

template<class N >

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

inlinevirtual

Implements bpp::Tree.

Definition at line 116 of file TreeTemplate.h.

Referenced by bpp::TreeTemplate< N >::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 104 of file TreeTemplate.h.

deleteDistanceToFather()

template<class N >

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

inlinevirtual

Implements bpp::Tree.

Definition at line 192 of file TreeTemplate.h.

References bpp::TreeTemplate< N >::getNode().

deleteNodeName()

template<class N >

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

inlinevirtual

Implements bpp::Tree.

Definition at line 178 of file TreeTemplate.h.

References bpp::TreeTemplate< N >::getNode().

getAncestorsId()

template<class N >

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

inlinevirtual

Implements bpp::Tree.

Definition at line 166 of file TreeTemplate.h.

References bpp::TreeTemplateTools::getAncestorsId(), and bpp::TreeTemplate< N >::getNode().

getBranchesId()

template<class N >

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

inlinevirtual

Implements bpp::Tree.

Definition at line 143 of file TreeTemplate.h.

References bpp::TreeTemplateTools::getNodesId(), bpp::TreeTemplate< N >::getRootId(), and bpp::TreeTemplate< N >::root_.

getBranchLengths() [1/2]

template<class N >

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

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 329 of file TreeTemplate.h.

References bpp::TreeTemplateTools::getBranchLengths(), and bpp::TreeTemplate< N >::root_.

getBranchLengths() [2/2]

template<class N >

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

inlinevirtual

Implements bpp::Tree.

Definition at line 160 of file TreeTemplate.h.

References bpp::TreeTemplateTools::getBranchLengths(), and bpp::TreeTemplate< N >::root_.

getBranchProperty() [1/2]

template<class N >

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

inlinevirtual

Implements bpp::Tree.

Definition at line 212 of file TreeTemplate.h.

References bpp::TreeTemplate< N >::getNode().

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

getBranchProperty() [2/2]

template<class N >

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

inlinevirtual

Implements bpp::Tree.

Definition at line 214 of file TreeTemplate.h.

References bpp::TreeTemplate< N >::getNode().

getBranchPropertyNames()

template<class N >

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

inlinevirtual

Implements bpp::Tree.

Definition at line 218 of file TreeTemplate.h.

References bpp::TreeTemplate< N >::getNode().

getDistanceToFather()

template<class N >

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

inlinevirtual

Implements bpp::Tree.

Definition at line 188 of file TreeTemplate.h.

References bpp::TreeTemplate< N >::getNode().

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

getFatherId()

template<class N >

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

inlinevirtual

Implements bpp::Tree.

Definition at line 168 of file TreeTemplate.h.

References bpp::TreeTemplate< N >::getNode().

getInnerNodes() [1/2]

template<class N >

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

inlinevirtual

Definition at line 403 of file TreeTemplate.h.

References bpp::TreeTemplateTools::getInnerNodes(), and bpp::TreeTemplate< N >::root_.

getInnerNodes() [2/2]

template<class N >

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

inlinevirtual

Definition at line 401 of file TreeTemplate.h.

References bpp::TreeTemplateTools::getInnerNodes(), and bpp::TreeTemplate< N >::root_.

getInnerNodesId()

template<class N >

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

inlinevirtual

Implements bpp::Tree.

Definition at line 141 of file TreeTemplate.h.

References bpp::TreeTemplateTools::getInnerNodesId(), and bpp::TreeTemplate< N >::root_.

getLeafId()

template<class N >

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

inlinevirtual

Implements bpp::Tree.

Definition at line 135 of file TreeTemplate.h.

References bpp::TreeTemplateTools::getLeafId(), and bpp::TreeTemplate< N >::root_.

getLeaves() [1/2]

template<class N >

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

inlinevirtual

Definition at line 395 of file TreeTemplate.h.

References bpp::TreeTemplateTools::getLeaves(), and bpp::TreeTemplate< N >::root_.

getLeaves() [2/2]

template<class N >

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

inlinevirtual

Definition at line 393 of file TreeTemplate.h.

References bpp::TreeTemplateTools::getLeaves(), and bpp::TreeTemplate< N >::root_.

getLeavesId()

template<class N >

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

inlinevirtual

Implements bpp::Tree.

Definition at line 137 of file TreeTemplate.h.

References bpp::TreeTemplateTools::getLeavesId(), and bpp::TreeTemplate< N >::root_.

getLeavesNames()

template<class N >

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

inlinevirtual

Implements bpp::Tree.

Definition at line 162 of file TreeTemplate.h.

References bpp::TreeTemplateTools::getLeavesNames(), and bpp::TreeTemplate< N >::root_.

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

getName()

template<class N >

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

inlinevirtual

Methods:

Implements bpp::Tree.

Definition at line 123 of file TreeTemplate.h.

References bpp::TreeTemplate< N >::name_.

getNextId()

template<class N >

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

inlinevirtual

Get an id.

Returns

an unused node id.

Implements bpp::Tree.

Definition at line 369 of file TreeTemplate.h.

References bpp::TreeTools::getMPNUId(), and bpp::TreeTemplate< N >::root_.

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

getNode() [1/4]

template<class N >

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

inlinevirtual

Definition at line 445 of file TreeTemplate.h.

References bpp::TreeTemplate< N >::root_, and bpp::TreeTemplateTools::searchNodeWithName().

getNode() [2/4]

template<class N >

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

inlinevirtual

Definition at line 454 of file TreeTemplate.h.

References bpp::TreeTemplate< N >::root_.

getNode() [3/4]

template<class N >

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

inlinevirtual

Definition at line 405 of file TreeTemplate.h.

References bpp::TreeTemplate< N >::root_, bpp::TreeTemplateTools::searchFirstNodeWithId(), and bpp::TextTools::toString().

Referenced by bpp::LegacySubstitutionMappingTools::computeCountsPerSitePerBranchPerType(), bpp::LegacySubstitutionMappingTools::computeCountsPerSitePerType(), bpp::LegacySubstitutionMappingTools::computeCountsPerTypePerBranch(), bpp::TreeTemplate< N >::deleteDistanceToFather(), bpp::TreeTemplate< N >::deleteNodeName(), bpp::TreeTemplateTools::dropLeaf(), bpp::TreeTemplate< N >::getAncestorsId(), bpp::TreeTemplate< N >::getBranchProperty(), bpp::TreeTemplate< N >::getBranchPropertyNames(), bpp::TreeTemplate< N >::getDistanceToFather(), bpp::TreeTemplate< N >::getFatherId(), bpp::TreeTemplate< N >::getNodeName(), bpp::TreeTemplate< N >::getNodeProperty(), bpp::TreeTemplate< N >::getNodePropertyNames(), bpp::TreeTemplate< N >::getSonsId(), bpp::TreeTemplate< N >::hasBranchProperty(), bpp::TreeTemplate< N >::hasDistanceToFather(), bpp::TreeTemplate< N >::hasFather(), bpp::TreeTemplate< N >::hasNodeName(), bpp::TreeTemplate< N >::hasNodeProperty(), bpp::TreeTemplate< N >::hasNoSon(), bpp::TreeTemplate< N >::isLeaf(), bpp::TreeTemplate< N >::isRoot(), bpp::TreeTemplate< N >::newOutGroup(), bpp::TreeTemplate< N >::removeBranchProperty(), bpp::TreeTemplate< N >::removeNodeProperty(), bpp::TreeTemplate< N >::rootAt(), bpp::TreeTemplate< N >::setBranchProperty(), bpp::TreeTemplate< N >::setDistanceToFather(), bpp::TreeTemplate< N >::setNodeName(), and bpp::TreeTemplate< N >::setNodeProperty().

getNode() [4/4]

template<class N >

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

inlinevirtual

Definition at line 425 of file TreeTemplate.h.

References bpp::TreeTemplate< N >::root_, bpp::TreeTemplateTools::searchFirstNodeWithId(), and bpp::TextTools::toString().

getNodeName()

template<class N >

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

inlinevirtual

Implements bpp::Tree.

Definition at line 172 of file TreeTemplate.h.

References bpp::TreeTemplate< N >::getNode().

getNodeProperty() [1/2]

template<class N >

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

inlinevirtual

Implements bpp::Tree.

Definition at line 200 of file TreeTemplate.h.

References bpp::TreeTemplate< N >::getNode().

getNodeProperty() [2/2]

template<class N >

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

inlinevirtual

Implements bpp::Tree.

Definition at line 202 of file TreeTemplate.h.

References bpp::TreeTemplate< N >::getNode().

getNodePropertyNames()

template<class N >

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

inlinevirtual

Implements bpp::Tree.

Definition at line 206 of file TreeTemplate.h.

References bpp::TreeTemplate< N >::getNode().

getNodes() [1/2]

template<class N >

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

inlinevirtual

Definition at line 399 of file TreeTemplate.h.

References bpp::TreeTemplateTools::getNodes(), and bpp::TreeTemplate< N >::root_.

getNodes() [2/2]

template<class N >

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

inlinevirtual

Definition at line 397 of file TreeTemplate.h.

References bpp::TreeTemplateTools::getNodes(), and bpp::TreeTemplate< N >::root_.

Referenced by bpp::LegacyRewardMappingTools::computeRewardVectors(), bpp::LegacySubstitutionMappingTools::computeSubstitutionVectors(), bpp::LegacySubstitutionMappingTools::computeSubstitutionVectorsMarginal(), bpp::LegacySubstitutionMappingTools::computeSubstitutionVectorsNoAveraging(), bpp::LegacySubstitutionMappingTools::computeSubstitutionVectorsNoAveragingMarginal(), bpp::TreeTemplate< N >::resetNodesId(), bpp::NNITopologySearch::searchBetter(), bpp::NNITopologySearch::searchFast(), and bpp::NNITopologySearch::searchPhyML().

getNodesId()

template<class N >

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

inlinevirtual

Implements bpp::Tree.

Definition at line 139 of file TreeTemplate.h.

References bpp::TreeTemplateTools::getNodesId(), and bpp::TreeTemplate< N >::root_.

getNumberOfBranches()

template<class N >

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

inlinevirtual

Implements bpp::Tree.

Definition at line 133 of file TreeTemplate.h.

References bpp::TreeTemplateTools::getNumberOfBranches(), and bpp::TreeTemplate< N >::root_.

getNumberOfLeaves()

template<class N >

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

inlinevirtual

Implements bpp::Tree.

Definition at line 129 of file TreeTemplate.h.

References bpp::TreeTemplateTools::getNumberOfLeaves(), and bpp::TreeTemplate< N >::root_.

getNumberOfNodes()

template<class N >

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

inlinevirtual

Implements bpp::Tree.

Definition at line 131 of file TreeTemplate.h.

References bpp::TreeTemplateTools::getNumberOfNodes(), and bpp::TreeTemplate< N >::root_.

getRootId()

template<class N >

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

inlinevirtual

Implements bpp::Tree.

Definition at line 127 of file TreeTemplate.h.

References bpp::TreeTemplate< N >::root_.

Referenced by bpp::LegacyRewardMappingTools::computeRewardVectors(), bpp::LegacySubstitutionMappingTools::computeSubstitutionVectors(), bpp::TreeTemplate< N >::getBranchesId(), bpp::TreeTemplateTools::midRoot(), and bpp::TreeTemplate< N >::newOutGroup().

getRootNode() [1/2]

template<class N >

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

inlinevirtual

Definition at line 389 of file TreeTemplate.h.

References bpp::TreeTemplate< N >::root_.

Referenced by bpp::BipartitionList::BipartitionList(), bpp::PhyloTreeTools::buildFromTreeTemplate(), bpp::GlobalClockTreeLikelihoodFunctionWrapper::fireParameterChanged(), bpp::TreeTemplateTools::getDistanceMatrix(), bpp::TreeTemplateTools::getRadius(), bpp::TreeTemplate< N >::hasSameTopologyAs(), bpp::GlobalClockTreeLikelihoodFunctionWrapper::initParameters_(), bpp::TreeTemplateTools::midRoot(), bpp::TreeTemplate< N >::operator=(), bpp::PhyloStatistics::setTree(), bpp::TreeTemplate< N >::TreeTemplate(), 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 391 of file TreeTemplate.h.

References bpp::TreeTemplate< N >::root_.

getSonsId()

template<class N >

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

inlinevirtual

Implements bpp::Tree.

Definition at line 164 of file TreeTemplate.h.

References bpp::TreeTemplate< N >::getNode().

getTotalLength()

template<class N >

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

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 340 of file TreeTemplate.h.

References bpp::TreeTemplateTools::getTotalLength(), and bpp::TreeTemplate< N >::root_.

hasBranchProperty()

template<class N >

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

inlinevirtual

Implements bpp::Tree.

Definition at line 208 of file TreeTemplate.h.

References bpp::TreeTemplate< N >::getNode().

hasDistanceToFather()

template<class N >

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

inlinevirtual

Implements bpp::Tree.

Definition at line 194 of file TreeTemplate.h.

References bpp::TreeTemplate< N >::getNode().

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

hasFather()

template<class N >

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

inlinevirtual

Implements bpp::Tree.

Definition at line 170 of file TreeTemplate.h.

References bpp::TreeTemplate< N >::getNode().

hasNode()

template<class N >

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

inlinevirtual

Implements bpp::Tree.

Definition at line 180 of file TreeTemplate.h.

References bpp::TreeTemplateTools::hasNodeWithId(), and bpp::TreeTemplate< N >::root_.

hasNodeName()

template<class N >

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

inlinevirtual

Implements bpp::Tree.

Definition at line 174 of file TreeTemplate.h.

References bpp::TreeTemplate< N >::getNode().

hasNodeProperty()

template<class N >

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

inlinevirtual

Implements bpp::Tree.

Definition at line 196 of file TreeTemplate.h.

References bpp::TreeTemplate< N >::getNode().

hasNoSon()

template<class N >

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

inlinevirtual

Implements bpp::Tree.

Definition at line 184 of file TreeTemplate.h.

References bpp::TreeTemplate< N >::getNode().

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 permitted. 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 302 of file TreeTemplate.h.

References bpp::TreeTemplate< N >::clone(), bpp::TreeTemplate< N >::getRootNode(), bpp::TreeTemplateTools::haveSameOrderedTopology(), and bpp::TreeTemplateTools::orderTree().

isLeaf()

template<class N >

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

inlinevirtual

Implements bpp::Tree.

Definition at line 182 of file TreeTemplate.h.

References bpp::TreeTemplate< N >::getNode().

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 277 of file TreeTemplate.h.

References bpp::TreeTemplateTools::isMultifurcating(), and bpp::TreeTemplate< N >::root_.

isRoot()

template<class N >

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

inlinevirtual

Implements bpp::Tree.

Definition at line 186 of file TreeTemplate.h.

References bpp::TreeTemplate< N >::getNode(), and bpp::TreeTemplateTools::isRoot().

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 224 of file TreeTemplate.h.

References bpp::TreeTemplate< N >::root_.

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

newOutGroup() [1/2]

template<class N >

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

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 222 of file TreeTemplate.h.

References bpp::TreeTemplate< N >::getNode(), and bpp::TreeTemplate< N >::newOutGroup().

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

newOutGroup() [2/2]

template<class N >

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

inline

Definition at line 491 of file TreeTemplate.h.

References bpp::TreeTemplate< N >::getNextId(), bpp::TreeTemplate< N >::getRootId(), bpp::TreeTemplate< N >::isRooted(), bpp::TreeTemplate< N >::root_, bpp::TreeTemplate< N >::rootAt(), and bpp::TreeTemplate< N >::unroot().

operator=()

template<class N >

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

inline

Definition at line 95 of file TreeTemplate.h.

References bpp::TreeTemplateTools::deleteSubtree(), bpp::TreeTemplate< N >::getRootNode(), bpp::TreeTemplate< N >::name_, and bpp::TreeTemplate< N >::root_.

removeBranchProperty()

template<class N >

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

inlinevirtual

Implements bpp::Tree.

Definition at line 216 of file TreeTemplate.h.

References bpp::TreeTemplate< N >::getNode().

removeNodeProperty()

template<class N >

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

inlinevirtual

Implements bpp::Tree.

Definition at line 204 of file TreeTemplate.h.

References bpp::TreeTemplate< N >::getNode().

resetNodesId()

template<class N >

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

inlinevirtual

Number nodes.

Implements bpp::Tree.

Definition at line 268 of file TreeTemplate.h.

References bpp::TreeTemplate< N >::getNodes().

rootAt() [1/2]

template<class N >

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

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 220 of file TreeTemplate.h.

References bpp::TreeTemplate< N >::getNode(), and bpp::TreeTemplate< N >::rootAt().

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

rootAt() [2/2]

template<class N >

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

inline

Definition at line 463 of file TreeTemplate.h.

References bpp::TreeTemplate< N >::getBranchProperty(), bpp::TreeTemplate< N >::getDistanceToFather(), bpp::TreeTemplateTools::getPathBetweenAnyTwoNodes(), bpp::TreeTemplate< N >::hasDistanceToFather(), bpp::TreeTemplate< N >::isRooted(), bpp::TreeTemplate< N >::root_, and bpp::TreeTemplate< N >::unroot().

scaleTree()

template<class N >

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

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 361 of file TreeTemplate.h.

References bpp::TreeTemplate< N >::root_, and bpp::TreeTemplateTools::scaleTree().

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 345 of file TreeTemplate.h.

References bpp::TreeTemplate< N >::root_, and bpp::TreeTemplateTools::setBranchLengths().

setBranchProperty()

template<class N >

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

inlinevirtual

Implements bpp::Tree.

Definition at line 210 of file TreeTemplate.h.

References bpp::TreeTemplate< N >::getNode().

setDistanceToFather()

template<class N >

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

inlinevirtual

Implements bpp::Tree.

Definition at line 190 of file TreeTemplate.h.

References bpp::TreeTemplate< N >::getNode().

setName()

template<class N >

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

inlinevirtual

Implements bpp::Tree.

Definition at line 125 of file TreeTemplate.h.

References bpp::TreeTemplate< N >::name_.

setNodeName()

template<class N >

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

inlinevirtual

Implements bpp::Tree.

Definition at line 176 of file TreeTemplate.h.

References bpp::TreeTemplate< N >::getNode().

setNodeProperty()

template<class N >

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

inlinevirtual

Implements bpp::Tree.

Definition at line 198 of file TreeTemplate.h.

References bpp::TreeTemplate< N >::getNode().

setRootNode()

template<class N >

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

inlinevirtual

Definition at line 387 of file TreeTemplate.h.

References bpp::TreeTemplate< N >::root_.

Referenced by bpp::TreeTemplateTools::dropLeaf(), bpp::TreeTemplateTools::dropSubtree(), and bpp::TreeTemplate< N >::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 353 of file TreeTemplate.h.

References bpp::TreeTemplate< N >::root_, and bpp::TreeTemplateTools::setVoidBranchLengths().

swapNodes() [1/2]

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

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  )

inline

Definition at line 374 of file TreeTemplate.h.

References bpp::TreeTemplate< N >::root_, and bpp::TextTools::toString().

unroot()

template<class N >

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

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 226 of file TreeTemplate.h.

References bpp::TreeTemplate< N >::isRooted(), bpp::TreeTemplate< N >::root_, and bpp::TreeTemplate< N >::setRootNode().

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

Member Data Documentation

name_

template<class N >

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

private

Definition at line 66 of file TreeTemplate.h.

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

root_

template<class N >

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

private

Fields:

Definition at line 65 of file TreeTemplate.h.

Referenced by bpp::TreeTemplate< N >::getBranchesId(), bpp::TreeTemplate< N >::getBranchLengths(), bpp::TreeTemplate< N >::getInnerNodes(), bpp::TreeTemplate< N >::getInnerNodesId(), bpp::TreeTemplate< N >::getLeafId(), bpp::TreeTemplate< N >::getLeaves(), bpp::TreeTemplate< N >::getLeavesId(), bpp::TreeTemplate< N >::getLeavesNames(), bpp::TreeTemplate< N >::getNextId(), bpp::TreeTemplate< N >::getNode(), bpp::TreeTemplate< N >::getNodes(), bpp::TreeTemplate< N >::getNodesId(), bpp::TreeTemplate< N >::getNumberOfBranches(), bpp::TreeTemplate< N >::getNumberOfLeaves(), bpp::TreeTemplate< N >::getNumberOfNodes(), bpp::TreeTemplate< N >::getRootId(), bpp::TreeTemplate< N >::getRootNode(), bpp::TreeTemplate< N >::getTotalLength(), bpp::TreeTemplate< N >::hasNode(), bpp::TreeTemplate< N >::isMultifurcating(), bpp::TreeTemplate< N >::isRooted(), bpp::TreeTemplate< N >::newOutGroup(), bpp::TreeTemplate< N >::operator=(), bpp::TreeTemplate< N >::rootAt(), bpp::TreeTemplate< N >::scaleTree(), bpp::TreeTemplate< N >::setBranchLengths(), bpp::TreeTemplate< N >::setRootNode(), bpp::TreeTemplate< N >::setVoidBranchLengths(), bpp::TreeTemplate< N >::swapNodes(), bpp::TreeTemplate< N >::TreeTemplate(), bpp::TreeTemplate< N >::unroot(), and bpp::TreeTemplate< N >::~TreeTemplate().

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

• Bpp/Phyl/Tree/BipartitionList.h
• Bpp/Phyl/Tree/TreeTemplate.h