Interface for phylogenetic tree objects. More...

#include <Bpp/Phyl/Tree.h>

Inheritance diagram for bpp::Tree:

Collaboration diagram for bpp::Tree:

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 More...

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. More...

virtual void	newOutGroup (int nodeId)=0 throw (NodeNotFoundException)
	Root a tree by specifying an outgroup. More...

virtual bool	isRooted () const =0
	Tell if the tree is rooted. More...

virtual bool	unroot ()=0 throw (UnrootedTreeException)
	Unroot a rooted tree. More...

virtual void	resetNodesId ()=0
	Number nodes. More...

virtual bool	isMultifurcating () const =0
	Tell if the tree is multifurcating. More...

virtual std::vector< double >	getBranchLengths ()=0 throw (NodeException)
	Get all the branch lengths of a tree. More...

virtual double	getTotalLength ()=0 throw (NodeException)
	Get the total length (sum of all branch lengths) of a tree. More...

virtual void	setBranchLengths (double brLen)=0
	Set all the branch lengths of a tree. More...

virtual void	setVoidBranchLengths (double brLen)=0
	Give a length to branches that don't have one in a tree. More...

virtual void	scaleTree (double factor)=0 throw (NodeException)
	Scale a given tree. More...

virtual int	getNextId ()=0
	Get an id. More...


virtual std::string	getName () const =0
	Tree name. More...

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. More...

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

◆ Tree()

bpp::Tree::Tree ( )

inline

Definition at line 154 of file Tree.h.

◆ ~Tree()

virtual bpp::Tree::~Tree ( )

inlinevirtual

Definition at line 155 of file Tree.h.

Member Function Documentation

◆ clone()

Tree* bpp::Tree::clone ( ) const

pure virtual

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

◆ cloneSubtree()

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< bpp::Node >, and bpp::TreeTemplate< bpp::NodeTemplate >.

◆ deleteDistanceToFather()

virtual void bpp::Tree::deleteDistanceToFather ( int nodeId )

pure virtual

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

◆ deleteNodeName()

virtual void bpp::Tree::deleteNodeName	(	int	nodeId	)
throw	(	NodeNotFoundException
	)

pure virtual

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

◆ getAncestorsId()

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

pure virtual

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

◆ getBranchesId()

virtual std::vector<int> bpp::Tree::getBranchesId ( ) const

pure virtual

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

◆ getBranchLengths() [1/2]

virtual std::vector<double> bpp::Tree::getBranchLengths ( ) const

pure virtual

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

◆ getBranchLengths() [2/2]

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< bpp::Node >, and bpp::TreeTemplate< bpp::NodeTemplate >.

◆ getBranchProperty() [1/2]

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

pure virtual

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

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

◆ getBranchProperty() [2/2]

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

pure virtual

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

◆ getBranchPropertyNames()

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

pure virtual

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

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

◆ getDistanceToFather()

virtual double bpp::Tree::getDistanceToFather ( int nodeId ) const

pure virtual

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

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_().

◆ getFatherId()

virtual int bpp::Tree::getFatherId	(	int	parentId	)	const
throw	(	NodeNotFoundException
	)

pure virtual

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

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

◆ getInnerNodesId()

virtual std::vector<int> bpp::Tree::getInnerNodesId ( ) const

pure virtual

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

◆ getLeafId()

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

pure virtual

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

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

◆ getLeavesId()

virtual std::vector<int> bpp::Tree::getLeavesId ( ) const

pure virtual

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

◆ getLeavesNames()

virtual std::vector<std::string> bpp::Tree::getLeavesNames ( ) const

pure virtual

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

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

◆ getName()

virtual std::string bpp::Tree::getName ( ) const

pure virtual

Tree name.

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

◆ getNextId()

virtual int bpp::Tree::getNextId ( )

pure virtual

Get an id.

Returns: an unused node id.

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

◆ getNodeName()

virtual std::string bpp::Tree::getNodeName	(	int	nodeId	)	const
throw	(	NodeNotFoundException
	)

pure virtual

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

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

◆ getNodeProperty() [1/2]

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

pure virtual

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

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

◆ getNodeProperty() [2/2]

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

pure virtual

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

◆ getNodePropertyNames()

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

pure virtual

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

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

◆ getNodesId()

virtual std::vector<int> bpp::Tree::getNodesId ( ) const

pure virtual

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

◆ getNumberOfLeaves()

virtual size_t bpp::Tree::getNumberOfLeaves ( ) const

pure virtual

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

◆ getNumberOfNodes()

virtual size_t bpp::Tree::getNumberOfNodes ( ) const

pure virtual

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

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

◆ getRootId()

virtual int bpp::Tree::getRootId ( ) const

pure virtual

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

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

◆ getSonsId()

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

pure virtual

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

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().

◆ getTotalLength()

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< bpp::Node >, and bpp::TreeTemplate< bpp::NodeTemplate >.

◆ hasBranchProperty()

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

pure virtual

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

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

◆ hasDistanceToFather()

virtual bool bpp::Tree::hasDistanceToFather ( int nodeId ) const

pure virtual

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

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

◆ hasFather()

virtual bool bpp::Tree::hasFather	(	int	nodeId	)	const
throw	(	NodeNotFoundException
	)

pure virtual

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

◆ hasNode()

virtual bool bpp::Tree::hasNode ( int nodeId ) const

pure virtual

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

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

◆ hasNodeName()

virtual bool bpp::Tree::hasNodeName	(	int	nodeId	)	const
throw	(	NodeNotFoundException
	)

pure virtual

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

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

◆ hasNodeProperty()

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

pure virtual

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

◆ isLeaf()

virtual bool bpp::Tree::isLeaf	(	int	nodeId	)	const
throw	(	NodeNotFoundException
	)

pure virtual

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

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

◆ isMultifurcating()

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< bpp::Node >, and bpp::TreeTemplate< bpp::NodeTemplate >.

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

◆ isRoot()

virtual bool bpp::Tree::isRoot	(	int	nodeId	)	const
throw	(	NodeNotFoundException
	)

pure virtual

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

◆ isRooted()

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< bpp::Node >, and bpp::TreeTemplate< bpp::NodeTemplate >.

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

◆ newOutGroup()

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< bpp::Node >, and bpp::TreeTemplate< bpp::NodeTemplate >.

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

◆ removeBranchProperty()

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

pure virtual

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

◆ removeNodeProperty()

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

pure virtual

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

◆ resetNodesId()

virtual void bpp::Tree::resetNodesId ( )

pure virtual

Number nodes.

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

◆ rootAt()

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< bpp::Node >, and bpp::TreeTemplate< bpp::NodeTemplate >.

◆ scaleTree()

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< bpp::Node >, and bpp::TreeTemplate< bpp::NodeTemplate >.

◆ setBranchLengths()

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< bpp::Node >, and bpp::TreeTemplate< bpp::NodeTemplate >.

◆ setBranchProperty()

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< bpp::Node >, and bpp::TreeTemplate< bpp::NodeTemplate >.

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

◆ setDistanceToFather()

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

pure virtual

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

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

◆ setName()

virtual void bpp::Tree::setName ( const std::string & name )

pure virtual

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

◆ setNodeName()

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

pure virtual

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

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

◆ setNodeProperty()

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< bpp::Node >, and bpp::TreeTemplate< bpp::NodeTemplate >.

◆ setVoidBranchLengths()

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< bpp::Node >, and bpp::TreeTemplate< bpp::NodeTemplate >.

◆ swapNodes()

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

◆ unroot()

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< bpp::Node >, and bpp::TreeTemplate< bpp::NodeTemplate >.

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

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

Bpp/Phyl/Tree.h

Public Member Functions

Detailed Description

Constructor & Destructor Documentation

◆ Tree()

◆ ~Tree()

Member Function Documentation

◆ clone()

◆ cloneSubtree()

◆ deleteDistanceToFather()

◆ deleteNodeName()

◆ getAncestorsId()

◆ getBranchesId()

◆ getBranchLengths() [1/2]

◆ getBranchLengths() [2/2]

◆ getBranchProperty() [1/2]

◆ getBranchProperty() [2/2]

◆ getBranchPropertyNames()

◆ getDistanceToFather()

◆ getFatherId()

◆ getInnerNodesId()

◆ getLeafId()

◆ getLeavesId()

◆ getLeavesNames()

◆ getName()

◆ getNextId()

◆ getNodeName()

◆ getNodeProperty() [1/2]

◆ getNodeProperty() [2/2]

◆ getNodePropertyNames()

◆ getNodesId()

◆ getNumberOfLeaves()

◆ getNumberOfNodes()

◆ getRootId()

◆ getSonsId()

◆ getTotalLength()

◆ hasBranchProperty()

◆ hasDistanceToFather()

◆ hasFather()

◆ hasNode()

◆ hasNodeName()

◆ hasNodeProperty()

◆ isLeaf()

◆ isMultifurcating()

◆ isRoot()

◆ isRooted()

◆ newOutGroup()

◆ removeBranchProperty()

◆ removeNodeProperty()

◆ resetNodesId()

◆ rootAt()

◆ scaleTree()

◆ setBranchLengths()

◆ setBranchProperty()

◆ setDistanceToFather()

◆ setName()

◆ setNodeName()

◆ setNodeProperty()

◆ setVoidBranchLengths()

◆ swapNodes()

◆ unroot()