bpp::Tree Class Reference

Interface for phylogenetic tree objects. More...

#include <Bpp/Phyl/Tree.h>

Inheritance diagram for bpp::Tree:

Collaboration diagram for bpp::Tree:

List of all members.

Public Member Functions
	Tree ()
virtual	~Tree ()
Tree *	clone () const =0
virtual Tree *	cloneSubtree (int newRootId) const =0
	clones a Subtree rooted at given node Id
virtual size_t	getNumberOfLeaves () const =0
virtual size_t	getNumberOfNodes () const =0
virtual std::vector< double >	getBranchLengths () const =0
virtual std::vector< std::string >	getLeavesNames () const =0
virtual void	rootAt (int nodeId)=0 throw (NodeNotFoundException)
	Change the root node.
virtual void	newOutGroup (int nodeId)=0 throw (NodeNotFoundException)
	Root a tree by specifying an outgroup.
virtual bool	isRooted () const =0
	Tell if the tree is rooted.
virtual bool	unroot ()=0 throw (UnrootedTreeException)
	Unroot a rooted tree.
virtual void	resetNodesId ()=0
	Number nodes.
virtual bool	isMultifurcating () const =0
	Tell if the tree is multifurcating.
virtual std::vector< double >	getBranchLengths ()=0 throw (NodeException)
	Get all the branch lengths of a tree.
virtual double	getTotalLength ()=0 throw (NodeException)
	Get the total length (sum of all branch lengths) of a tree.
virtual void	setBranchLengths (double brLen)=0
	Set all the branch lengths of a tree.
virtual void	setVoidBranchLengths (double brLen)=0
	Give a length to branches that don't have one in a tree.
virtual void	scaleTree (double factor)=0 throw (NodeException)
	Scale a given tree.
virtual int	getNextId ()=0
	Get an id.
virtual std::string	getName () const =0
	Tree name.
virtual void	setName (const std::string &name)=0
Retrieving ids.
virtual int	getRootId () const =0
virtual int	getLeafId (const std::string &name) const =0 throw (NodeNotFoundException)
virtual std::vector< int >	getLeavesId () const =0
virtual std::vector< int >	getNodesId () const =0
virtual std::vector< int >	getInnerNodesId () const =0
virtual std::vector< int >	getBranchesId () const =0
virtual std::vector< int >	getSonsId (int parentId) const =0 throw (NodeNotFoundException)
virtual std::vector< int >	getAncestorsId (int nodeId) const =0 throw (NodeNotFoundException)
virtual int	getFatherId (int parentId) const =0 throw (NodeNotFoundException)
virtual bool	hasFather (int nodeId) const =0 throw (NodeNotFoundException)
Dealing with node names.
virtual std::string	getNodeName (int nodeId) const =0 throw (NodeNotFoundException)
virtual void	setNodeName (int nodeId, const std::string &name)=0 throw (NodeNotFoundException)
virtual void	deleteNodeName (int nodeId)=0 throw (NodeNotFoundException)
virtual bool	hasNodeName (int nodeId) const =0 throw (NodeNotFoundException)
Several tests.
virtual bool	hasNode (int nodeId) const =0
virtual bool	isLeaf (int nodeId) const =0 throw (NodeNotFoundException)
virtual bool	isRoot (int nodeId) const =0 throw (NodeNotFoundException)
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.
Dealing with branch lengths.
virtual double	getDistanceToFather (int nodeId) const =0
virtual void	setDistanceToFather (int nodeId, double length)=0
virtual void	deleteDistanceToFather (int nodeId)=0
virtual bool	hasDistanceToFather (int nodeId) const =0
Node properties.
virtual bool	hasNodeProperty (int nodeId, const std::string &name) const =0 throw (NodeNotFoundException)
virtual void	setNodeProperty (int nodeId, const std::string &name, const Clonable &property)=0 throw (NodeNotFoundException)
virtual Clonable *	getNodeProperty (int nodeId, const std::string &name)=0 throw (NodeNotFoundException)
virtual const Clonable *	getNodeProperty (int nodeId, const std::string &name) const =0 throw (NodeNotFoundException)
virtual Clonable *	removeNodeProperty (int nodeId, const std::string &name)=0 throw (NodeNotFoundException)
virtual std::vector< std::string >	getNodePropertyNames (int nodeId) const =0 throw (NodeNotFoundException)
Branch properties.
virtual bool	hasBranchProperty (int nodeId, const std::string &name) const =0 throw (NodeNotFoundException)
virtual void	setBranchProperty (int nodeId, const std::string &name, const Clonable &property)=0 throw (NodeNotFoundException)
virtual Clonable *	getBranchProperty (int nodeId, const std::string &name)=0 throw (NodeNotFoundException)
virtual const Clonable *	getBranchProperty (int nodeId, const std::string &name) const =0 throw (NodeNotFoundException)
virtual Clonable *	removeBranchProperty (int nodeId, const std::string &name)=0 throw (NodeNotFoundException)
virtual std::vector< std::string >	getBranchPropertyNames (int nodeId) const =0 throw (NodeNotFoundException)

---

Detailed Description

Interface for phylogenetic tree objects.

Definition at line 148 of file Tree.h.

---

Constructor & Destructor Documentation

bpp::Tree::Tree

(

)

[inline]

Definition at line 154 of file Tree.h.

virtual bpp::Tree::~Tree

(

)

[inline, virtual]

Definition at line 155 of file Tree.h.

---

Member Function Documentation

Tree* bpp::Tree::clone

(

)

const [pure virtual]

Implements bpp::Clonable.

Implemented in bpp::TreeTemplate< N >, bpp::TreeTemplate< Node >, bpp::TreeTemplate< INode >, and bpp::TreeTemplate< SNode >.

virtual Tree* bpp::Tree::cloneSubtree

(

int

newRootId

)

const [pure virtual]

clones a Subtree rooted at given node Id

Implemented in bpp::TreeTemplate< N >, bpp::TreeTemplate< Node >, bpp::TreeTemplate< INode >, and bpp::TreeTemplate< SNode >.

virtual void bpp::Tree::deleteDistanceToFather

(

int

nodeId

)

[pure virtual]

Implemented in bpp::TreeTemplate< N >, bpp::TreeTemplate< Node >, bpp::TreeTemplate< INode >, and bpp::TreeTemplate< SNode >.

virtual void bpp::Tree::deleteNodeName

(

int

nodeId

)

throw (NodeNotFoundException) [pure virtual]

Implemented in bpp::TreeTemplate< N >, bpp::TreeTemplate< Node >, bpp::TreeTemplate< INode >, and bpp::TreeTemplate< SNode >.

virtual std::vector<int> bpp::Tree::getAncestorsId

(

int

nodeId

)

const throw (NodeNotFoundException) [pure virtual]

Implemented in bpp::TreeTemplate< N >, bpp::TreeTemplate< Node >, bpp::TreeTemplate< INode >, and bpp::TreeTemplate< SNode >.

virtual std::vector<int> bpp::Tree::getBranchesId

(

)

const [pure virtual]

Implemented in bpp::TreeTemplate< N >, bpp::TreeTemplate< Node >, bpp::TreeTemplate< INode >, and bpp::TreeTemplate< SNode >.

virtual std::vector<double> bpp::Tree::getBranchLengths

(

)

const [pure virtual]

Implemented in bpp::TreeTemplate< N >, bpp::TreeTemplate< Node >, bpp::TreeTemplate< INode >, and bpp::TreeTemplate< SNode >.

virtual std::vector<double> bpp::Tree::getBranchLengths

(

)

throw (NodeException) [pure virtual]

Get all the branch lengths of a tree.

Returns:

A vector with all branch lengths.

Exceptions:

NodeException

If a branch length is lacking.

Implemented in bpp::TreeTemplate< N >, bpp::TreeTemplate< Node >, bpp::TreeTemplate< INode >, and bpp::TreeTemplate< SNode >.

virtual Clonable* bpp::Tree::getBranchProperty	(	int	nodeId,
		const std::string &	name
	)		throw (NodeNotFoundException) [pure virtual]

Implemented in bpp::TreeTemplate< N >, bpp::TreeTemplate< Node >, bpp::TreeTemplate< INode >, and bpp::TreeTemplate< SNode >.

Referenced by bpp::BootstrapValuesTreeDrawingListener::afterDrawBranch(), bpp::TreeTemplateTools::cloneSubtree(), and bpp::TreeTools::treeToParenthesis().

virtual const Clonable* bpp::Tree::getBranchProperty	(	int	nodeId,
		const std::string &	name
	)		const throw (NodeNotFoundException) [pure virtual]

Implemented in bpp::TreeTemplate< N >, bpp::TreeTemplate< Node >, bpp::TreeTemplate< INode >, and bpp::TreeTemplate< SNode >.

virtual std::vector<std::string> bpp::Tree::getBranchPropertyNames

(

int

nodeId

)

const throw (NodeNotFoundException) [pure virtual]

Implemented in bpp::TreeTemplate< N >, bpp::TreeTemplate< Node >, bpp::TreeTemplate< INode >, and bpp::TreeTemplate< SNode >.

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

virtual double bpp::Tree::getDistanceToFather

(

int

nodeId

)

const [pure virtual]

Implemented in bpp::TreeTemplate< N >, bpp::TreeTemplate< Node >, bpp::TreeTemplate< INode >, and bpp::TreeTemplate< SNode >.

Referenced by bpp::BranchLengthsTreeDrawingListener::afterDrawBranch(), bpp::TreeTemplateTools::cloneSubtree(), bpp::TreeTools::constrainedMidPointRooting(), bpp::TreeTools::convertToClockTree(), bpp::TreeTools::convertToClockTree2(), bpp::TreeTools::getDistanceBetweenAnyTwoNodes(), bpp::TreeTools::midpointRooting(), and bpp::TreeTools::statFromNode_().

virtual int bpp::Tree::getFatherId

(

int

parentId

)

const throw (NodeNotFoundException) [pure virtual]

Implemented in bpp::TreeTemplate< N >, bpp::TreeTemplate< Node >, bpp::TreeTemplate< INode >, and bpp::TreeTemplate< SNode >.

Referenced by bpp::TreeTools::midpointRooting().

virtual std::vector<int> bpp::Tree::getInnerNodesId

(

)

const [pure virtual]

Implemented in bpp::TreeTemplate< N >, bpp::TreeTemplate< Node >, bpp::TreeTemplate< INode >, and bpp::TreeTemplate< SNode >.

virtual int bpp::Tree::getLeafId

(

const std::string &

name

)

const throw (NodeNotFoundException) [pure virtual]

Implemented in bpp::TreeTemplate< N >, bpp::TreeTemplate< Node >, bpp::TreeTemplate< INode >, and bpp::TreeTemplate< SNode >.

Referenced by bpp::TreeTools::getDistanceMatrix(), and bpp::TreeTools::midpointRooting().

virtual std::vector<int> bpp::Tree::getLeavesId

(

)

const [pure virtual]

Implemented in bpp::TreeTemplate< N >, bpp::TreeTemplate< Node >, bpp::TreeTemplate< INode >, and bpp::TreeTemplate< SNode >.

virtual std::vector<std::string> bpp::Tree::getLeavesNames

(

)

const [pure virtual]

Implemented in bpp::TreeTemplate< N >, bpp::TreeTemplate< Node >, bpp::TreeTemplate< INode >, and bpp::TreeTemplate< SNode >.

Referenced by bpp::BipartitionList::BipartitionList(), bpp::TreeTools::getDistanceMatrix(), and bpp::TreeTools::haveSameTopology().

virtual std::string bpp::Tree::getName

(

)

const [pure virtual]

Tree name.

Implemented in bpp::TreeTemplate< N >, bpp::TreeTemplate< Node >, bpp::TreeTemplate< INode >, and bpp::TreeTemplate< SNode >.

virtual int bpp::Tree::getNextId

(

)

[pure virtual]

Get an id.

Returns:

an unused node id.

Implemented in bpp::TreeTemplate< N >, bpp::TreeTemplate< Node >, bpp::TreeTemplate< INode >, and bpp::TreeTemplate< SNode >.

virtual std::string bpp::Tree::getNodeName

(

int

nodeId

)

const throw (NodeNotFoundException) [pure virtual]

Implemented in bpp::TreeTemplate< N >, bpp::TreeTemplate< Node >, bpp::TreeTemplate< INode >, and bpp::TreeTemplate< SNode >.

Referenced by bpp::LeafNamesTreeDrawingListener::afterDrawNode(), bpp::LabelInnerNodesTreeDrawingListener::afterDrawNode(), bpp::LabelCollapsedNodesTreeDrawingListener::afterDrawNode(), bpp::TreeTemplateTools::cloneSubtree(), bpp::SiteSimulationResult::getLeaveNames(), bpp::TreeTools::treeToParenthesis(), and bpp::NexusIOTree::write_().

virtual Clonable* bpp::Tree::getNodeProperty	(	int	nodeId,
		const std::string &	name
	)		throw (NodeNotFoundException) [pure virtual]

Implemented in bpp::TreeTemplate< N >, bpp::TreeTemplate< Node >, bpp::TreeTemplate< INode >, and bpp::TreeTemplate< SNode >.

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

virtual const Clonable* bpp::Tree::getNodeProperty	(	int	nodeId,
		const std::string &	name
	)		const throw (NodeNotFoundException) [pure virtual]

Implemented in bpp::TreeTemplate< N >, bpp::TreeTemplate< Node >, bpp::TreeTemplate< INode >, and bpp::TreeTemplate< SNode >.

virtual std::vector<std::string> bpp::Tree::getNodePropertyNames

(

int

nodeId

)

const throw (NodeNotFoundException) [pure virtual]

Implemented in bpp::TreeTemplate< N >, bpp::TreeTemplate< Node >, bpp::TreeTemplate< INode >, and bpp::TreeTemplate< SNode >.

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

virtual std::vector<int> bpp::Tree::getNodesId

(

)

const [pure virtual]

Implemented in bpp::TreeTemplate< N >, bpp::TreeTemplate< Node >, bpp::TreeTemplate< INode >, and bpp::TreeTemplate< SNode >.

virtual size_t bpp::Tree::getNumberOfLeaves

(

)

const [pure virtual]

Implemented in bpp::TreeTemplate< N >, bpp::TreeTemplate< Node >, bpp::TreeTemplate< INode >, and bpp::TreeTemplate< SNode >.

virtual size_t bpp::Tree::getNumberOfNodes

(

)

const [pure virtual]

Implemented in bpp::TreeTemplate< N >, bpp::TreeTemplate< Node >, bpp::TreeTemplate< INode >, and bpp::TreeTemplate< SNode >.

Referenced by bpp::BipartitionList::BipartitionList().

virtual int bpp::Tree::getRootId

(

)

const [pure virtual]

Implemented in bpp::TreeTemplate< N >, bpp::TreeTemplate< Node >, bpp::TreeTemplate< INode >, and bpp::TreeTemplate< SNode >.

Referenced by bpp::TreeTools::constrainedMidPointRooting(), bpp::TreeTools::initBranchLengthsGrafen(), bpp::TreeTools::midpointRooting(), bpp::SiteSimulationResult::SiteSimulationResult(), bpp::TreeTemplate< SNode >::TreeTemplate(), and bpp::TreeTools::treeToParenthesis().

virtual std::vector<int> bpp::Tree::getSonsId

(

int

parentId

)

const throw (NodeNotFoundException) [pure virtual]

Implemented in bpp::TreeTemplate< N >, bpp::TreeTemplate< Node >, bpp::TreeTemplate< INode >, and bpp::TreeTemplate< SNode >.

Referenced by bpp::TreeTemplateTools::cloneSubtree(), bpp::TreeTools::constrainedMidPointRooting(), bpp::TreeTools::convertToClockTree(), bpp::TreeTools::convertToClockTree2(), bpp::TreeTools::getMaxId(), bpp::RNonHomogeneousMixedTreeLikelihood::init(), bpp::TreeTools::midpointRooting(), bpp::TreeTools::statFromNode_(), and bpp::TreeTools::treeToParenthesis().

virtual double bpp::Tree::getTotalLength

(

)

throw (NodeException) [pure virtual]

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.

Implemented in bpp::TreeTemplate< N >, bpp::TreeTemplate< Node >, bpp::TreeTemplate< INode >, and bpp::TreeTemplate< SNode >.

virtual bool bpp::Tree::hasBranchProperty	(	int	nodeId,
		const std::string &	name
	)		const throw (NodeNotFoundException) [pure virtual]

Implemented in bpp::TreeTemplate< N >, bpp::TreeTemplate< Node >, bpp::TreeTemplate< INode >, and bpp::TreeTemplate< SNode >.

Referenced by bpp::BootstrapValuesTreeDrawingListener::afterDrawBranch(), and bpp::TreeTools::treeToParenthesis().

virtual bool bpp::Tree::hasDistanceToFather

(

int

nodeId

)

const [pure virtual]

Implemented in bpp::TreeTemplate< N >, bpp::TreeTemplate< Node >, bpp::TreeTemplate< INode >, and bpp::TreeTemplate< SNode >.

Referenced by bpp::BranchLengthsTreeDrawingListener::afterDrawBranch(), bpp::TreeTemplateTools::cloneSubtree(), bpp::TreeTools::convertToClockTree(), and bpp::TreeTools::convertToClockTree2().

virtual bool bpp::Tree::hasFather

(

int

nodeId

)

const throw (NodeNotFoundException) [pure virtual]

Implemented in bpp::TreeTemplate< N >, bpp::TreeTemplate< Node >, bpp::TreeTemplate< INode >, and bpp::TreeTemplate< SNode >.

virtual bool bpp::Tree::hasNode

(

int

nodeId

)

const [pure virtual]

Implemented in bpp::TreeTemplate< N >, bpp::TreeTemplate< Node >, bpp::TreeTemplate< INode >, and bpp::TreeTemplate< SNode >.

Referenced by bpp::TreeTools::convertToClockTree(), bpp::TreeTools::convertToClockTree2(), and bpp::TreeTools::getDistanceBetweenAnyTwoNodes().

virtual bool bpp::Tree::hasNodeName

(

int

nodeId

)

const throw (NodeNotFoundException) [pure virtual]

Implemented in bpp::TreeTemplate< N >, bpp::TreeTemplate< Node >, bpp::TreeTemplate< INode >, and bpp::TreeTemplate< SNode >.

Referenced by bpp::LabelInnerNodesTreeDrawingListener::afterDrawNode(), bpp::LabelCollapsedNodesTreeDrawingListener::afterDrawNode(), and bpp::TreeTemplateTools::cloneSubtree().

virtual bool bpp::Tree::hasNodeProperty	(	int	nodeId,
		const std::string &	name
	)		const throw (NodeNotFoundException) [pure virtual]

Implemented in bpp::TreeTemplate< N >, bpp::TreeTemplate< Node >, bpp::TreeTemplate< INode >, and bpp::TreeTemplate< SNode >.

virtual bool bpp::Tree::isLeaf

(

int

nodeId

)

const throw (NodeNotFoundException) [pure virtual]

Implemented in bpp::TreeTemplate< N >, bpp::TreeTemplate< Node >, bpp::TreeTemplate< INode >, and bpp::TreeTemplate< SNode >.

Referenced by bpp::LeafNamesTreeDrawingListener::afterDrawNode(), bpp::TreeTools::computeBootstrapValues(), bpp::DRTreeLikelihoodTools::getPosteriorProbabilitiesForEachStateForEachRate(), bpp::TreeTools::statFromNode_(), and bpp::TreeTools::treeToParenthesis().

virtual bool bpp::Tree::isMultifurcating

(

)

const [pure virtual]

Tell if the tree is multifurcating.

Returns:

True if the tree is multifurcating.

Implemented in bpp::TreeTemplate< N >, bpp::TreeTemplate< Node >, bpp::TreeTemplate< INode >, and bpp::TreeTemplate< SNode >.

Referenced by bpp::TreeTools::constrainedMidPointRooting().

virtual bool bpp::Tree::isRoot

(

int

nodeId

)

const throw (NodeNotFoundException) [pure virtual]

Implemented in bpp::TreeTemplate< N >, bpp::TreeTemplate< Node >, bpp::TreeTemplate< INode >, and bpp::TreeTemplate< SNode >.

virtual bool bpp::Tree::isRooted

(

)

const [pure virtual]

Tell if the tree is rooted.

Returns:

True if the tree is rooted.

Implemented in bpp::TreeTemplate< N >, bpp::TreeTemplate< Node >, bpp::TreeTemplate< INode >, and bpp::TreeTemplate< SNode >.

Referenced by bpp::BipartitionList::BipartitionList(), bpp::TreeTools::constrainedMidPointRooting(), and bpp::TreeTools::midpointRooting().

virtual void bpp::Tree::newOutGroup

(

int

nodeId

)

throw (NodeNotFoundException) [pure virtual]

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.

Implemented in bpp::TreeTemplate< N >, bpp::TreeTemplate< Node >, bpp::TreeTemplate< INode >, and bpp::TreeTemplate< SNode >.

Referenced by bpp::TreeTools::midpointRooting().

virtual Clonable* bpp::Tree::removeBranchProperty	(	int	nodeId,
		const std::string &	name
	)		throw (NodeNotFoundException) [pure virtual]

Implemented in bpp::TreeTemplate< N >, bpp::TreeTemplate< Node >, bpp::TreeTemplate< INode >, and bpp::TreeTemplate< SNode >.

virtual Clonable* bpp::Tree::removeNodeProperty	(	int	nodeId,
		const std::string &	name
	)		throw (NodeNotFoundException) [pure virtual]

Implemented in bpp::TreeTemplate< N >, bpp::TreeTemplate< Node >, bpp::TreeTemplate< INode >, and bpp::TreeTemplate< SNode >.

virtual void bpp::Tree::resetNodesId

(

)

[pure virtual]

Number nodes.

Implemented in bpp::TreeTemplate< N >, bpp::TreeTemplate< Node >, bpp::TreeTemplate< INode >, and bpp::TreeTemplate< SNode >.

virtual void bpp::Tree::rootAt

(

int

nodeId

)

throw (NodeNotFoundException) [pure virtual]

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.

Implemented in bpp::TreeTemplate< N >, bpp::TreeTemplate< Node >, bpp::TreeTemplate< INode >, and bpp::TreeTemplate< SNode >.

virtual void bpp::Tree::scaleTree

(

double

factor

)

throw (NodeException) [pure virtual]

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.

Implemented in bpp::TreeTemplate< N >, bpp::TreeTemplate< Node >, bpp::TreeTemplate< INode >, and bpp::TreeTemplate< SNode >.

virtual void bpp::Tree::setBranchLengths

(

double

brLen

)

[pure virtual]

Set all the branch lengths of a tree.

Parameters:

brLen

The branch length to apply.

Implemented in bpp::TreeTemplate< N >, bpp::TreeTemplate< Node >, bpp::TreeTemplate< INode >, and bpp::TreeTemplate< SNode >.

virtual void bpp::Tree::setBranchProperty	(	int	nodeId,
		const std::string &	name,
		const Clonable &	property
	)		throw (NodeNotFoundException) [pure virtual]

Implemented in bpp::TreeTemplate< N >, bpp::TreeTemplate< Node >, bpp::TreeTemplate< INode >, and bpp::TreeTemplate< SNode >.

Referenced by bpp::TreeTools::computeBootstrapValues().

virtual void bpp::Tree::setDistanceToFather	(	int	nodeId,
		double	length
	)		[pure virtual]

Implemented in bpp::TreeTemplate< N >, bpp::TreeTemplate< Node >, bpp::TreeTemplate< INode >, and bpp::TreeTemplate< SNode >.

Referenced by bpp::TreeTools::constrainedMidPointRooting(), bpp::TreeTools::convertToClockTree(), and bpp::TreeTools::midpointRooting().

virtual void bpp::Tree::setName

(

const std::string &

name

)

[pure virtual]

Implemented in bpp::TreeTemplate< N >, bpp::TreeTemplate< Node >, bpp::TreeTemplate< INode >, and bpp::TreeTemplate< SNode >.

virtual void bpp::Tree::setNodeName	(	int	nodeId,
		const std::string &	name
	)		throw (NodeNotFoundException) [pure virtual]

Implemented in bpp::TreeTemplate< N >, bpp::TreeTemplate< Node >, bpp::TreeTemplate< INode >, and bpp::TreeTemplate< SNode >.

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

virtual void bpp::Tree::setNodeProperty	(	int	nodeId,
		const std::string &	name,
		const Clonable &	property
	)		throw (NodeNotFoundException) [pure virtual]

Implemented in bpp::TreeTemplate< N >, bpp::TreeTemplate< Node >, bpp::TreeTemplate< INode >, and bpp::TreeTemplate< SNode >.

virtual void bpp::Tree::setVoidBranchLengths

(

double

brLen

)

[pure virtual]

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

Parameters:

brLen

The branch length to apply.

Implemented in bpp::TreeTemplate< N >, bpp::TreeTemplate< Node >, bpp::TreeTemplate< INode >, and bpp::TreeTemplate< SNode >.

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

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

virtual bool bpp::Tree::unroot

(

)

throw (UnrootedTreeException) [pure virtual]

Unroot a rooted tree.

Returns:

True if the tree has been unrooted.

Exceptions:

UnrootedTreeException

If the tree is already rooted.

Implemented in bpp::TreeTemplate< N >, bpp::TreeTemplate< Node >, bpp::TreeTemplate< INode >, and bpp::TreeTemplate< SNode >.

Referenced by bpp::TreeTools::midpointRooting().

---

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

• Bpp/Phyl/Tree.h