bpp::Node Class Reference

The phylogenetic node class. More...

#include <Bpp/Phyl/Node.h>

Inheritance diagram for bpp::Node:

Collaboration diagram for bpp::Node:

Public Member Functions
	Node ()
	Build a new void Node object. More...
	Node (int id)
	Build a new Node with specified id. More...
	Node (const std::string &name)
	Build a new Node with specified name. More...
	Node (int id, const std::string &name)
	Build a new Node with specified id and name. More...
	Node (const Node &node)
	Copy constructor. More...
Node &	operator= (const Node &node)
	Assignation operator. More...
Node *	clone () const
virtual	~Node ()
std::vector< const Node * >	getNeighbors () const
std::vector< Node * >	getNeighbors ()
virtual size_t	degree () const
virtual bool	operator== (const Node &node) const
virtual bool	isLeaf () const
Identity
virtual int	getId () const
	Get the node's id. More...
virtual void	setId (int id)
	Set this node's id. More...
virtual std::vector< int >	getSonsId () const
Name:
virtual std::string	getName () const throw (NodePException)
	Get the name associated to this node, if there is one, otherwise throw a NodeException. More...
virtual void	setName (const std::string &name)
	Give a name or update the name associated to the node. More...
virtual void	deleteName ()
	Delete the name associated to this node (do nothing if there is no name). More...
virtual bool	hasName () const
	Tell is this node has a name. More...
Distances:
virtual double	getDistanceToFather () const
	Get the distance to the father node is there is one, otherwise throw a NodeException. More...
virtual void	setDistanceToFather (double distance)
	Set or update the distance toward the father node. More...
virtual void	deleteDistanceToFather ()
	Delete the distance to the father node. More...
virtual bool	hasDistanceToFather () const
	Tell is this node has a distance to the father. More...
Father:
virtual const Node *	getFather () const
	Get the father of this node is there is one. More...
virtual Node *	getFather ()
	Get the father of this node is there is one. More...
virtual int	getFatherId () const
virtual void	setFather (Node *node) throw (NullPointerException)
	Set the father node of this node. More...
virtual Node *	removeFather ()
	Remove the father of this node. More...
virtual bool	hasFather () const
	Tell if this node has a father node. More...
Sons:
virtual size_t	getNumberOfSons () const
virtual std::vector< Node * > &	getSons ()
virtual const Node *	getSon (size_t pos) const throw (IndexOutOfBoundsException)
virtual Node *	getSon (size_t pos) throw (IndexOutOfBoundsException)
virtual void	addSon (size_t pos, Node *node) throw (NullPointerException, NodePException)
virtual void	addSon (Node *node) throw (NullPointerException, NodePException)
virtual void	setSon (size_t pos, Node *node) throw (IndexOutOfBoundsException, NullPointerException, NodePException)
virtual Node *	removeSon (size_t pos) throw (IndexOutOfBoundsException)
virtual void	removeSon (Node *node) throw (NodeNotFoundException, NullPointerException)
virtual void	removeSons ()
virtual void	swap (size_t branch1, size_t branch2) throw (IndexOutOfBoundsException)
virtual size_t	getSonPosition (const Node *son) const throw (NodeNotFoundException, NullPointerException)
Operators:
a positive value send the corresponding son; a negative value send the father.
Node *	operator[] (int i)
const Node *	operator[] (int i) const
Node properties:
virtual void	setNodeProperty (const std::string &name, const Clonable &property)
	Set/add a node property. More...
virtual Clonable *	getNodeProperty (const std::string &name) throw (PropertyNotFoundException)
virtual const Clonable *	getNodeProperty (const std::string &name) const throw (PropertyNotFoundException)
virtual Clonable *	removeNodeProperty (const std::string &name) throw (PropertyNotFoundException)
virtual void	deleteNodeProperty (const std::string &name) throw (PropertyNotFoundException)
virtual void	removeNodeProperties ()
	Remove all node properties. More...
virtual void	deleteNodeProperties ()
	Delete all node properties. More...
virtual bool	hasNodeProperty (const std::string &name) const
virtual std::vector< std::string >	getNodePropertyNames () const
Branch properties:
virtual void	setBranchProperty (const std::string &name, const Clonable &property)
	Set/add a branch property. More...
virtual Clonable *	getBranchProperty (const std::string &name) throw (PropertyNotFoundException)
virtual const Clonable *	getBranchProperty (const std::string &name) const throw (PropertyNotFoundException)
virtual Clonable *	removeBranchProperty (const std::string &name) throw (PropertyNotFoundException)
virtual void	deleteBranchProperty (const std::string &name) throw (PropertyNotFoundException)
virtual void	removeBranchProperties ()
	Remove all branch properties. More...
virtual void	deleteBranchProperties ()
	Delete all branch properties. More...
virtual bool	hasBranchProperty (const std::string &name) const
virtual std::vector< std::string >	getBranchPropertyNames () const
virtual bool	hasBootstrapValue () const
virtual double	getBootstrapValue () const throw (PropertyNotFoundException)

Protected Attributes
int	id_
std::string *	name_
std::vector< Node * >	sons_
Node *	father_
double *	distanceToFather_
std::map< std::string, Clonable * >	nodeProperties_
std::map< std::string, Clonable * >	branchProperties_

Detailed Description

The phylogenetic node class.

This class is for use with the TreeTemplate class, an implementation of the Tree interface. TreeTemplates are made made of nodes, instances of this class. Since trees are oriented (rooted), 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.

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

• An identity tag, to identity it in the tree;
• A name, necessary for leaf nodes, optionnal else;
• A pointer toward the father node;
• A std::vector of pointer toward son nodes;
• The distance from the father node:
• A property map, that may contain any information to link to each node, e.g. bootstrap value or GC content.

Methods are provided to help the building of trees from scratch. Trees are more easily built from root to leaves: The addSon(Node) method adds a node to the list of direct descendants of a given node. The son node will also have its father set to the current node. It is also possible to build a tree starting from the leaves using the setFather method. Changing the parent node will automatically append the current node to the son nodes of the new father.

See Also

Tree, TreeTemplate

Definition at line 89 of file Node.h.

Constructor & Destructor Documentation

bpp::Node::Node ( )

inline

Build a new void Node object.

Definition at line 105 of file Node.h.

Referenced by clone().

bpp::Node::Node ( int  id )

inline

Build a new Node with specified id.

Definition at line 118 of file Node.h.

bpp::Node::Node ( const std::string &  name )

inline

Build a new Node with specified name.

Definition at line 131 of file Node.h.

bpp::Node::Node ( int  id, const std::string &  name  )

inline

Build a new Node with specified id and name.

Definition at line 144 of file Node.h.

Node::Node

(

const Node &

node

)

Copy constructor.

Warning

This constructor copies all fields, excepted father and son node pointers.

Parameters

node	The node to copy.

Copy constructor:

Definition at line 56 of file Node.cpp.

References branchProperties_, branchProperties_, branchProperties_, distanceToFather_, distanceToFather_, hasDistanceToFather(), hasName(), name_, name_, nodeProperties_, nodeProperties_, and nodeProperties_.

virtual bpp::Node::~Node ( )

inlinevirtual

Definition at line 176 of file Node.h.

References branchProperties_, branchProperties_, distanceToFather_, distanceToFather_, name_, name_, nodeProperties_, and nodeProperties_.

Member Function Documentation

virtual void bpp::Node::addSon ( size_t  pos, Node *  node  ) throw (NullPointerException, NodePException)

inlinevirtual

Definition at line 406 of file Node.h.

References sons_, sons_, sons_, and sons_.

Referenced by bpp::DRTreeParsimonyScore::doNNI(), bpp::DRTreeParsimonyScore::doNNI(), bpp::NNIHomogeneousTreeLikelihood::doNNI(), bpp::NNIHomogeneousTreeLikelihood::doNNI(), bpp::HierarchicalClustering::finalStep(), bpp::HierarchicalClustering::finalStep(), bpp::PGMA::finalStep(), bpp::PGMA::finalStep(), bpp::NeighborJoining::finalStep(), bpp::NeighborJoining::finalStep(), bpp::NeighborJoining::finalStep(), bpp::NeighborJoining::finalStep(), bpp::NeighborJoining::finalStep(), bpp::HierarchicalClustering::getParentNode(), bpp::HierarchicalClustering::getParentNode(), bpp::PGMA::getParentNode(), bpp::PGMA::getParentNode(), bpp::AbstractAgglomerativeDistanceMethod::getParentNode(), bpp::AbstractAgglomerativeDistanceMethod::getParentNode(), bpp::TreeTemplateTools::getRandomTree(), bpp::TreeTemplateTools::getRandomTree(), bpp::TreeTemplateTools::getRandomTree(), bpp::TreeTemplateTools::midRoot(), bpp::TreeTemplateTools::midRoot(), bpp::Nhx::parenthesisToNode(), bpp::TreeTemplateTools::parenthesisToNode(), and bpp::BipartitionList::toTree().

virtual void bpp::Node::addSon ( Node *  node ) throw (NullPointerException, NodePException)

inlinevirtual

Definition at line 418 of file Node.h.

References sons_, sons_, sons_, and sons_.

Node* bpp::Node::clone ( ) const

inline

Definition at line 173 of file Node.h.

References Node().

virtual size_t bpp::Node::degree ( ) const

inlinevirtual

Definition at line 487 of file Node.h.

References getNumberOfSons(), and hasFather().

Referenced by bpp::DRTreeParsimonyScore::computeScoresForNode(), bpp::DRTreeParsimonyScore::computeScoresPostorderForNode(), bpp::DRTreeParsimonyScore::computeScoresPreorderForNode(), and isLeaf().

virtual void bpp::Node::deleteBranchProperties ( )

inlinevirtual

Delete all branch properties.

Definition at line 668 of file Node.h.

References branchProperties_, branchProperties_, and branchProperties_.

virtual void bpp::Node::deleteBranchProperty ( const std::string &  name ) throw (PropertyNotFoundException)

inlinevirtual

Definition at line 644 of file Node.h.

References branchProperties_, branchProperties_, and hasBranchProperty().

Referenced by bpp::Nhx::changeNamesToTags(), and bpp::Nhx::changeTagsToNames().

virtual void bpp::Node::deleteDistanceToFather ( )

inlinevirtual

Delete the distance to the father node.

Definition at line 308 of file Node.h.

References distanceToFather_, distanceToFather_, and distanceToFather_.

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

virtual void bpp::Node::deleteName ( )

inlinevirtual

Delete the name associated to this node (do nothing if there is no name).

Definition at line 255 of file Node.h.

References name_, name_, and name_.

virtual void bpp::Node::deleteNodeProperties ( )

inlinevirtual

Delete all node properties.

Definition at line 578 of file Node.h.

References nodeProperties_, nodeProperties_, and nodeProperties_.

virtual void bpp::Node::deleteNodeProperty ( const std::string &  name ) throw (PropertyNotFoundException)

inlinevirtual

Definition at line 554 of file Node.h.

References hasNodeProperty(), nodeProperties_, and nodeProperties_.

Referenced by bpp::Nhx::changeNamesToTags(), and bpp::Nhx::changeTagsToNames().

double Node::getBootstrapValue ( ) const throw (PropertyNotFoundException)

virtual

Definition at line 146 of file Node.cpp.

References bpp::TreeTools::BOOTSTRAP, getBranchProperty(), and hasBranchProperty().

virtual Clonable* bpp::Node::getBranchProperty ( const std::string &  name ) throw (PropertyNotFoundException)

inlinevirtual

Definition at line 616 of file Node.h.

References branchProperties_, and hasBranchProperty().

Referenced by bpp::BootstrapValuesTreeDrawingListener::afterDrawBranch(), bpp::Nhx::changeNamesToTags(), bpp::Nhx::changeTagsToNames(), getBootstrapValue(), bpp::TreeTemplateTools::getBranchProperties(), bpp::TreeTemplateTools::getBranchProperties(), bpp::TreeTemplateTools::nodeToParenthesis(), bpp::TreeTemplateTools::nodeToParenthesis(), bpp::TreeTemplateTools::nodeToParenthesis(), bpp::Nhx::propertiesToParenthesis(), bpp::TreeTemplateTools::treeToParenthesis(), and bpp::TreeTemplateTools::treeToParenthesis().

virtual const Clonable* bpp::Node::getBranchProperty ( const std::string &  name ) const throw (PropertyNotFoundException)

inlinevirtual

Definition at line 624 of file Node.h.

References branchProperties_, and hasBranchProperty().

virtual std::vector<std::string> bpp::Node::getBranchPropertyNames ( ) const

inlinevirtual

Definition at line 679 of file Node.h.

References bpp::MapTools::getKeys().

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

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

inlinevirtual

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

Returns

The distance to the father node.

Definition at line 282 of file Node.h.

References distanceToFather_, and hasDistanceToFather().

Referenced by bpp::BranchLengthsTreeDrawingListener::afterDrawBranch(), bpp::PhyloStatistics::computeForSubtree_(), bpp::PhyloStatistics::computeForSubtree_(), bpp::SubstitutionMappingTools::computeSubstitutionVectors(), bpp::SubstitutionMappingTools::computeSubstitutionVectorsMarginal(), bpp::SubstitutionMappingTools::computeSubstitutionVectorsNoAveraging(), bpp::SubstitutionMappingTools::computeSubstitutionVectorsNoAveragingMarginal(), bpp::AbstractHomogeneousTreeLikelihood::computeTransitionProbabilitiesForNode(), bpp::AbstractNonHomogeneousTreeLikelihood::computeTransitionProbabilitiesForNode(), bpp::RNonHomogeneousMixedTreeLikelihood::computeTransitionProbabilitiesForNode(), bpp::NonHomogeneousSequenceSimulator::dEvolveInternal(), bpp::NonHomogeneousSequenceSimulator::evolve(), bpp::PhylogramDrawBranchEvent::getBranchCursor(), bpp::TreeTemplateTools::getHeight(), bpp::TreeTemplateTools::getHeights(), bpp::HierarchicalClustering::getParentNode(), bpp::PGMA::getParentNode(), bpp::TreeTemplateTools::getSubtreeMoments(), bpp::NonHomogeneousSequenceSimulator::init(), bpp::Nhx::nodeToParenthesis(), bpp::TreeTemplateTools::nodeToParenthesis(), bpp::TreeTemplateTools::nodeToParenthesis(), bpp::TreeTemplateTools::processDistsInSubtree_(), bpp::TreeTemplateTools::processDistsInSubtree_(), bpp::PhylogramPlot::recursivePlot_(), bpp::Nhx::treeToParenthesis(), and bpp::TreeTemplateTools::treeToParenthesis().

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

inlinevirtual

Get the father of this node is there is one.

Returns

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

Reimplemented in bpp::NodeTemplate< NodeInfos >.

Definition at line 338 of file Node.h.

References father_.

Referenced by bpp::BipartitionList::buildBitBipartitions(), bpp::BipartitionList::buildBitBipartitions(), bpp::BipartitionList::buildBitBipartitions(), bpp::RHomogeneousTreeLikelihood::computeDownSubtreeD2Likelihood(), bpp::RNonHomogeneousTreeLikelihood::computeDownSubtreeD2Likelihood(), bpp::RNonHomogeneousMixedTreeLikelihood::computeDownSubtreeD2Likelihood(), bpp::RHomogeneousTreeLikelihood::computeDownSubtreeDLikelihood(), bpp::RNonHomogeneousTreeLikelihood::computeDownSubtreeDLikelihood(), bpp::RNonHomogeneousMixedTreeLikelihood::computeDownSubtreeDLikelihood(), bpp::DRHomogeneousTreeLikelihood::computeLikelihoodAtNode_(), bpp::DRNonHomogeneousTreeLikelihood::computeLikelihoodAtNode_(), bpp::DRTreeParsimonyScore::computeScoresPostorderForNode(), bpp::DRTreeParsimonyScore::computeScoresPreorder(), bpp::SubstitutionMappingTools::computeSubstitutionVectors(), bpp::SubstitutionMappingTools::computeSubstitutionVectors(), bpp::SubstitutionMappingTools::computeSubstitutionVectorsMarginal(), bpp::SubstitutionMappingTools::computeSubstitutionVectorsNoAveraging(), bpp::SubstitutionMappingTools::computeSubstitutionVectorsNoAveraging(), bpp::SubstitutionMappingTools::computeSubstitutionVectorsNoAveragingMarginal(), bpp::DRHomogeneousTreeLikelihood::computeSubtreeLikelihoodPrefix(), bpp::DRHomogeneousTreeLikelihood::computeSubtreeLikelihoodPrefix(), bpp::DRNonHomogeneousTreeLikelihood::computeSubtreeLikelihoodPrefix(), bpp::DRNonHomogeneousTreeLikelihood::computeSubtreeLikelihoodPrefix(), bpp::RNonHomogeneousTreeLikelihood::computeTreeD2Likelihood(), bpp::RHomogeneousTreeLikelihood::computeTreeD2Likelihood(), bpp::RNonHomogeneousMixedTreeLikelihood::computeTreeD2Likelihood(), bpp::RNonHomogeneousMixedTreeLikelihood::computeTreeD2Likelihood(), bpp::DRHomogeneousTreeLikelihood::computeTreeD2LikelihoodAtNode(), bpp::DRNonHomogeneousTreeLikelihood::computeTreeD2LikelihoodAtNode(), bpp::RNonHomogeneousTreeLikelihood::computeTreeDLikelihood(), bpp::RHomogeneousTreeLikelihood::computeTreeDLikelihood(), bpp::RNonHomogeneousMixedTreeLikelihood::computeTreeDLikelihood(), bpp::RNonHomogeneousMixedTreeLikelihood::computeTreeDLikelihood(), bpp::DRHomogeneousTreeLikelihood::computeTreeDLikelihoodAtNode(), bpp::DRNonHomogeneousTreeLikelihood::computeTreeDLikelihoodAtNode(), bpp::DRHomogeneousTreeLikelihood::displayLikelihood(), bpp::DRNonHomogeneousTreeLikelihood::displayLikelihood(), bpp::DRTreeParsimonyScore::doNNI(), bpp::DRTreeParsimonyScore::doNNI(), bpp::NNIHomogeneousTreeLikelihood::doNNI(), bpp::NNIHomogeneousTreeLikelihood::doNNI(), bpp::TreeTemplateTools::getAncestorsId(), bpp::TreeTemplateTools::getPathBetweenAnyTwoNodes(), bpp::TreeTemplateTools::getPathBetweenAnyTwoNodes(), bpp::TreeTemplateTools::getPathBetweenAnyTwoNodes(), bpp::TreeTemplateTools::getPathBetweenAnyTwoNodes(), bpp::TreeTemplateTools::midRoot(), bpp::DRHomogeneousTreeLikelihood::resetLikelihoodArrays(), bpp::DRNonHomogeneousTreeLikelihood::resetLikelihoodArrays(), bpp::NNITopologySearch::searchBetter(), bpp::NNITopologySearch::searchBetter(), bpp::NNITopologySearch::searchFast(), bpp::NNITopologySearch::searchFast(), bpp::NNITopologySearch::searchPhyML(), bpp::NNITopologySearch::searchPhyML(), bpp::NNITopologySearch::searchPhyML(), bpp::NNITopologySearch::searchPhyML(), bpp::NNITopologySearch::searchPhyML(), bpp::NNITopologySearch::searchPhyML(), bpp::NNITopologySearch::searchPhyML(), bpp::DRTreeParsimonyScore::testNNI(), bpp::DRTreeParsimonyScore::testNNI(), bpp::NNIHomogeneousTreeLikelihood::testNNI(), bpp::NNIHomogeneousTreeLikelihood::testNNI(), bpp::NNIHomogeneousTreeLikelihood::testNNI(), bpp::NNIHomogeneousTreeLikelihood::testNNI(), and bpp::NNIHomogeneousTreeLikelihood::testNNI().

virtual Node* bpp::Node::getFather ( )

inlinevirtual

Get the father of this node is there is one.

Returns

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

Reimplemented in bpp::NodeTemplate< NodeInfos >.

Definition at line 345 of file Node.h.

References father_.

virtual int bpp::Node::getFatherId ( ) const

inlinevirtual

Definition at line 347 of file Node.h.

References father_.

virtual int bpp::Node::getId ( ) const

inlinevirtual

Get the node's id.

Returns

The identity tag of this node.

Definition at line 202 of file Node.h.

References id_.

Referenced by bpp::AbstractNonHomogeneousTreeLikelihood::AbstractNonHomogeneousTreeLikelihood(), bpp::BipartitionList::buildBitBipartitions(), bpp::RHomogeneousClockTreeLikelihood::computeBranchLengthsFromHeights(), bpp::GlobalClockTreeLikelihoodFunctionWrapper::computeBranchLengthsFromHeights_(), bpp::GlobalClockTreeLikelihoodFunctionWrapper::computeBranchLengthsFromHeights_(), bpp::GlobalClockTreeLikelihoodFunctionWrapper::computeBranchLengthsFromHeights_(), bpp::RHomogeneousTreeLikelihood::computeDownSubtreeD2Likelihood(), bpp::RHomogeneousTreeLikelihood::computeDownSubtreeD2Likelihood(), bpp::RHomogeneousTreeLikelihood::computeDownSubtreeD2Likelihood(), bpp::RHomogeneousTreeLikelihood::computeDownSubtreeD2Likelihood(), bpp::RHomogeneousTreeLikelihood::computeDownSubtreeD2Likelihood(), bpp::RHomogeneousTreeLikelihood::computeDownSubtreeD2Likelihood(), bpp::RNonHomogeneousTreeLikelihood::computeDownSubtreeD2Likelihood(), bpp::RNonHomogeneousTreeLikelihood::computeDownSubtreeD2Likelihood(), bpp::RNonHomogeneousTreeLikelihood::computeDownSubtreeD2Likelihood(), bpp::RNonHomogeneousTreeLikelihood::computeDownSubtreeD2Likelihood(), bpp::RNonHomogeneousTreeLikelihood::computeDownSubtreeD2Likelihood(), bpp::RNonHomogeneousTreeLikelihood::computeDownSubtreeD2Likelihood(), bpp::RNonHomogeneousMixedTreeLikelihood::computeDownSubtreeD2Likelihood(), bpp::RHomogeneousTreeLikelihood::computeDownSubtreeDLikelihood(), bpp::RHomogeneousTreeLikelihood::computeDownSubtreeDLikelihood(), bpp::RHomogeneousTreeLikelihood::computeDownSubtreeDLikelihood(), bpp::RHomogeneousTreeLikelihood::computeDownSubtreeDLikelihood(), bpp::RHomogeneousTreeLikelihood::computeDownSubtreeDLikelihood(), bpp::RHomogeneousTreeLikelihood::computeDownSubtreeDLikelihood(), bpp::RNonHomogeneousTreeLikelihood::computeDownSubtreeDLikelihood(), bpp::RNonHomogeneousTreeLikelihood::computeDownSubtreeDLikelihood(), bpp::RNonHomogeneousTreeLikelihood::computeDownSubtreeDLikelihood(), bpp::RNonHomogeneousTreeLikelihood::computeDownSubtreeDLikelihood(), bpp::RNonHomogeneousTreeLikelihood::computeDownSubtreeDLikelihood(), bpp::RNonHomogeneousTreeLikelihood::computeDownSubtreeDLikelihood(), bpp::RNonHomogeneousMixedTreeLikelihood::computeDownSubtreeDLikelihood(), bpp::DRHomogeneousTreeLikelihood::computeLikelihoodAtNode_(), bpp::DRHomogeneousTreeLikelihood::computeLikelihoodAtNode_(), bpp::DRHomogeneousTreeLikelihood::computeLikelihoodAtNode_(), bpp::DRHomogeneousTreeLikelihood::computeLikelihoodAtNode_(), bpp::DRNonHomogeneousTreeLikelihood::computeLikelihoodAtNode_(), bpp::DRNonHomogeneousTreeLikelihood::computeLikelihoodAtNode_(), bpp::DRNonHomogeneousTreeLikelihood::computeLikelihoodAtNode_(), bpp::DRNonHomogeneousTreeLikelihood::computeLikelihoodAtNode_(), bpp::DRNonHomogeneousTreeLikelihood::computeLikelihoodAtNode_(), bpp::DRHomogeneousTreeLikelihood::computeRootLikelihood(), bpp::DRHomogeneousTreeLikelihood::computeRootLikelihood(), bpp::DRHomogeneousTreeLikelihood::computeRootLikelihood(), bpp::DRHomogeneousTreeLikelihood::computeRootLikelihood(), bpp::DRNonHomogeneousTreeLikelihood::computeRootLikelihood(), bpp::DRNonHomogeneousTreeLikelihood::computeRootLikelihood(), bpp::DRNonHomogeneousTreeLikelihood::computeRootLikelihood(), bpp::DRNonHomogeneousTreeLikelihood::computeRootLikelihood(), bpp::DRTreeParsimonyScore::computeScoresForNode(), bpp::DRTreeParsimonyScore::computeScoresForNode(), bpp::DRTreeParsimonyScore::computeScoresPostorder(), bpp::DRTreeParsimonyScore::computeScoresPostorder(), bpp::DRTreeParsimonyScore::computeScoresPostorder(), bpp::DRTreeParsimonyScore::computeScoresPostorder(), bpp::DRTreeParsimonyScore::computeScoresPostorder(), bpp::DRTreeParsimonyScore::computeScoresPostorderForNode(), bpp::DRTreeParsimonyScore::computeScoresPostorderForNode(), bpp::DRTreeParsimonyScore::computeScoresPreorder(), bpp::DRTreeParsimonyScore::computeScoresPreorder(), bpp::DRTreeParsimonyScore::computeScoresPreorder(), bpp::DRTreeParsimonyScore::computeScoresPreorder(), bpp::DRTreeParsimonyScore::computeScoresPreorder(), bpp::DRTreeParsimonyScore::computeScoresPreorderForNode(), bpp::DRTreeParsimonyScore::computeScoresPreorderForNode(), bpp::SubstitutionMappingTools::computeSubstitutionVectors(), bpp::SubstitutionMappingTools::computeSubstitutionVectors(), bpp::SubstitutionMappingTools::computeSubstitutionVectors(), bpp::SubstitutionMappingTools::computeSubstitutionVectors(), bpp::SubstitutionMappingTools::computeSubstitutionVectors(), bpp::SubstitutionMappingTools::computeSubstitutionVectors(), bpp::SubstitutionMappingTools::computeSubstitutionVectors(), bpp::SubstitutionMappingTools::computeSubstitutionVectors(), bpp::SubstitutionMappingTools::computeSubstitutionVectors(), bpp::SubstitutionMappingTools::computeSubstitutionVectors(), bpp::SubstitutionMappingTools::computeSubstitutionVectors(), bpp::SubstitutionMappingTools::computeSubstitutionVectors(), bpp::SubstitutionMappingTools::computeSubstitutionVectors(), bpp::SubstitutionMappingTools::computeSubstitutionVectors(), bpp::SubstitutionMappingTools::computeSubstitutionVectorsMarginal(), bpp::SubstitutionMappingTools::computeSubstitutionVectorsMarginal(), bpp::SubstitutionMappingTools::computeSubstitutionVectorsMarginal(), bpp::SubstitutionMappingTools::computeSubstitutionVectorsNoAveraging(), bpp::SubstitutionMappingTools::computeSubstitutionVectorsNoAveraging(), bpp::SubstitutionMappingTools::computeSubstitutionVectorsNoAveraging(), bpp::SubstitutionMappingTools::computeSubstitutionVectorsNoAveraging(), bpp::SubstitutionMappingTools::computeSubstitutionVectorsNoAveraging(), bpp::SubstitutionMappingTools::computeSubstitutionVectorsNoAveraging(), bpp::SubstitutionMappingTools::computeSubstitutionVectorsNoAveraging(), bpp::SubstitutionMappingTools::computeSubstitutionVectorsNoAveraging(), bpp::SubstitutionMappingTools::computeSubstitutionVectorsNoAveraging(), bpp::SubstitutionMappingTools::computeSubstitutionVectorsNoAveraging(), bpp::SubstitutionMappingTools::computeSubstitutionVectorsNoAveraging(), bpp::SubstitutionMappingTools::computeSubstitutionVectorsNoAveraging(), bpp::SubstitutionMappingTools::computeSubstitutionVectorsNoAveraging(), bpp::SubstitutionMappingTools::computeSubstitutionVectorsNoAveraging(), bpp::SubstitutionMappingTools::computeSubstitutionVectorsNoAveragingMarginal(), bpp::SubstitutionMappingTools::computeSubstitutionVectorsNoAveragingMarginal(), bpp::SubstitutionMappingTools::computeSubstitutionVectorsNoAveragingMarginal(), bpp::RNonHomogeneousTreeLikelihood::computeSubtreeLikelihood(), bpp::RNonHomogeneousTreeLikelihood::computeSubtreeLikelihood(), bpp::RNonHomogeneousTreeLikelihood::computeSubtreeLikelihood(), bpp::RNonHomogeneousTreeLikelihood::computeSubtreeLikelihood(), bpp::RNonHomogeneousTreeLikelihood::computeSubtreeLikelihood(), bpp::RNonHomogeneousTreeLikelihood::computeSubtreeLikelihood(), bpp::RHomogeneousTreeLikelihood::computeSubtreeLikelihood(), bpp::RHomogeneousTreeLikelihood::computeSubtreeLikelihood(), bpp::RHomogeneousTreeLikelihood::computeSubtreeLikelihood(), bpp::RHomogeneousTreeLikelihood::computeSubtreeLikelihood(), bpp::RHomogeneousTreeLikelihood::computeSubtreeLikelihood(), bpp::RHomogeneousTreeLikelihood::computeSubtreeLikelihood(), bpp::RNonHomogeneousMixedTreeLikelihood::computeSubtreeLikelihood(), bpp::DRHomogeneousTreeLikelihood::computeSubtreeLikelihoodPostfix(), bpp::DRHomogeneousTreeLikelihood::computeSubtreeLikelihoodPostfix(), bpp::DRHomogeneousTreeLikelihood::computeSubtreeLikelihoodPostfix(), bpp::DRHomogeneousTreeLikelihood::computeSubtreeLikelihoodPostfix(), bpp::DRHomogeneousTreeLikelihood::computeSubtreeLikelihoodPostfix(), bpp::DRHomogeneousTreeLikelihood::computeSubtreeLikelihoodPostfix(), bpp::DRNonHomogeneousTreeLikelihood::computeSubtreeLikelihoodPostfix(), bpp::DRNonHomogeneousTreeLikelihood::computeSubtreeLikelihoodPostfix(), bpp::DRNonHomogeneousTreeLikelihood::computeSubtreeLikelihoodPostfix(), bpp::DRNonHomogeneousTreeLikelihood::computeSubtreeLikelihoodPostfix(), bpp::DRNonHomogeneousTreeLikelihood::computeSubtreeLikelihoodPostfix(), bpp::DRNonHomogeneousTreeLikelihood::computeSubtreeLikelihoodPostfix(), bpp::DRHomogeneousTreeLikelihood::computeSubtreeLikelihoodPrefix(), bpp::DRHomogeneousTreeLikelihood::computeSubtreeLikelihoodPrefix(), bpp::DRHomogeneousTreeLikelihood::computeSubtreeLikelihoodPrefix(), bpp::DRHomogeneousTreeLikelihood::computeSubtreeLikelihoodPrefix(), bpp::DRHomogeneousTreeLikelihood::computeSubtreeLikelihoodPrefix(), bpp::DRHomogeneousTreeLikelihood::computeSubtreeLikelihoodPrefix(), bpp::DRHomogeneousTreeLikelihood::computeSubtreeLikelihoodPrefix(), bpp::DRHomogeneousTreeLikelihood::computeSubtreeLikelihoodPrefix(), bpp::DRHomogeneousTreeLikelihood::computeSubtreeLikelihoodPrefix(), bpp::DRHomogeneousTreeLikelihood::computeSubtreeLikelihoodPrefix(), bpp::DRNonHomogeneousTreeLikelihood::computeSubtreeLikelihoodPrefix(), bpp::DRNonHomogeneousTreeLikelihood::computeSubtreeLikelihoodPrefix(), bpp::DRNonHomogeneousTreeLikelihood::computeSubtreeLikelihoodPrefix(), bpp::DRNonHomogeneousTreeLikelihood::computeSubtreeLikelihoodPrefix(), bpp::DRNonHomogeneousTreeLikelihood::computeSubtreeLikelihoodPrefix(), bpp::DRNonHomogeneousTreeLikelihood::computeSubtreeLikelihoodPrefix(), bpp::DRNonHomogeneousTreeLikelihood::computeSubtreeLikelihoodPrefix(), bpp::DRNonHomogeneousTreeLikelihood::computeSubtreeLikelihoodPrefix(), bpp::DRNonHomogeneousTreeLikelihood::computeSubtreeLikelihoodPrefix(), bpp::DRNonHomogeneousTreeLikelihood::computeSubtreeLikelihoodPrefix(), bpp::AbstractHomogeneousTreeLikelihood::computeTransitionProbabilitiesForNode(), bpp::AbstractHomogeneousTreeLikelihood::computeTransitionProbabilitiesForNode(), bpp::AbstractHomogeneousTreeLikelihood::computeTransitionProbabilitiesForNode(), bpp::AbstractNonHomogeneousTreeLikelihood::computeTransitionProbabilitiesForNode(), bpp::AbstractNonHomogeneousTreeLikelihood::computeTransitionProbabilitiesForNode(), bpp::AbstractNonHomogeneousTreeLikelihood::computeTransitionProbabilitiesForNode(), bpp::AbstractNonHomogeneousTreeLikelihood::computeTransitionProbabilitiesForNode(), bpp::RNonHomogeneousMixedTreeLikelihood::computeTransitionProbabilitiesForNode(), bpp::RNonHomogeneousMixedTreeLikelihood::computeTransitionProbabilitiesForNode(), bpp::RNonHomogeneousMixedTreeLikelihood::computeTransitionProbabilitiesForNode(), bpp::RNonHomogeneousMixedTreeLikelihood::computeTransitionProbabilitiesForNode(), bpp::RNonHomogeneousMixedTreeLikelihood::computeTransitionProbabilitiesForNode(), bpp::RNonHomogeneousTreeLikelihood::computeTreeD2Likelihood(), bpp::RNonHomogeneousTreeLikelihood::computeTreeD2Likelihood(), bpp::RNonHomogeneousTreeLikelihood::computeTreeD2Likelihood(), bpp::RNonHomogeneousTreeLikelihood::computeTreeD2Likelihood(), bpp::RNonHomogeneousTreeLikelihood::computeTreeD2Likelihood(), bpp::RNonHomogeneousTreeLikelihood::computeTreeD2Likelihood(), bpp::RNonHomogeneousTreeLikelihood::computeTreeD2Likelihood(), bpp::RNonHomogeneousTreeLikelihood::computeTreeD2Likelihood(), bpp::RNonHomogeneousTreeLikelihood::computeTreeD2Likelihood(), bpp::RNonHomogeneousTreeLikelihood::computeTreeD2Likelihood(), bpp::RHomogeneousTreeLikelihood::computeTreeD2Likelihood(), bpp::RHomogeneousTreeLikelihood::computeTreeD2Likelihood(), bpp::RHomogeneousTreeLikelihood::computeTreeD2Likelihood(), bpp::RHomogeneousTreeLikelihood::computeTreeD2Likelihood(), bpp::RHomogeneousTreeLikelihood::computeTreeD2Likelihood(), bpp::RHomogeneousTreeLikelihood::computeTreeD2Likelihood(), bpp::RNonHomogeneousTreeLikelihood::computeTreeD2Likelihood(), bpp::RNonHomogeneousTreeLikelihood::computeTreeD2Likelihood(), bpp::RNonHomogeneousTreeLikelihood::computeTreeD2Likelihood(), bpp::RNonHomogeneousTreeLikelihood::computeTreeD2Likelihood(), bpp::RNonHomogeneousTreeLikelihood::computeTreeD2Likelihood(), bpp::RNonHomogeneousTreeLikelihood::computeTreeD2Likelihood(), bpp::RNonHomogeneousTreeLikelihood::computeTreeD2Likelihood(), bpp::RNonHomogeneousTreeLikelihood::computeTreeD2Likelihood(), bpp::RNonHomogeneousTreeLikelihood::computeTreeD2Likelihood(), bpp::RNonHomogeneousTreeLikelihood::computeTreeD2Likelihood(), bpp::RNonHomogeneousTreeLikelihood::computeTreeD2Likelihood(), bpp::RNonHomogeneousTreeLikelihood::computeTreeD2Likelihood(), bpp::RNonHomogeneousTreeLikelihood::computeTreeD2Likelihood(), bpp::RNonHomogeneousTreeLikelihood::computeTreeD2Likelihood(), bpp::RNonHomogeneousTreeLikelihood::computeTreeD2Likelihood(), bpp::RNonHomogeneousTreeLikelihood::computeTreeD2Likelihood(), bpp::RNonHomogeneousTreeLikelihood::computeTreeD2Likelihood(), bpp::RNonHomogeneousTreeLikelihood::computeTreeD2Likelihood(), bpp::RNonHomogeneousTreeLikelihood::computeTreeD2Likelihood(), bpp::RNonHomogeneousTreeLikelihood::computeTreeD2Likelihood(), bpp::RNonHomogeneousTreeLikelihood::computeTreeD2Likelihood(), bpp::RNonHomogeneousTreeLikelihood::computeTreeD2Likelihood(), bpp::RNonHomogeneousMixedTreeLikelihood::computeTreeD2Likelihood(), bpp::RNonHomogeneousMixedTreeLikelihood::computeTreeD2Likelihood(), bpp::RNonHomogeneousMixedTreeLikelihood::computeTreeD2Likelihood(), bpp::DRHomogeneousTreeLikelihood::computeTreeD2LikelihoodAtNode(), bpp::DRHomogeneousTreeLikelihood::computeTreeD2LikelihoodAtNode(), bpp::DRHomogeneousTreeLikelihood::computeTreeD2LikelihoodAtNode(), bpp::DRHomogeneousTreeLikelihood::computeTreeD2LikelihoodAtNode(), bpp::DRHomogeneousTreeLikelihood::computeTreeD2LikelihoodAtNode(), bpp::DRNonHomogeneousTreeLikelihood::computeTreeD2LikelihoodAtNode(), bpp::DRNonHomogeneousTreeLikelihood::computeTreeD2LikelihoodAtNode(), bpp::DRNonHomogeneousTreeLikelihood::computeTreeD2LikelihoodAtNode(), bpp::DRNonHomogeneousTreeLikelihood::computeTreeD2LikelihoodAtNode(), bpp::DRNonHomogeneousTreeLikelihood::computeTreeD2LikelihoodAtNode(), bpp::RNonHomogeneousTreeLikelihood::computeTreeDLikelihood(), bpp::RNonHomogeneousTreeLikelihood::computeTreeDLikelihood(), bpp::RHomogeneousTreeLikelihood::computeTreeDLikelihood(), bpp::RHomogeneousTreeLikelihood::computeTreeDLikelihood(), bpp::RHomogeneousTreeLikelihood::computeTreeDLikelihood(), bpp::RHomogeneousTreeLikelihood::computeTreeDLikelihood(), bpp::RHomogeneousTreeLikelihood::computeTreeDLikelihood(), bpp::RHomogeneousTreeLikelihood::computeTreeDLikelihood(), bpp::RNonHomogeneousTreeLikelihood::computeTreeDLikelihood(), bpp::RNonHomogeneousTreeLikelihood::computeTreeDLikelihood(), bpp::RNonHomogeneousTreeLikelihood::computeTreeDLikelihood(), bpp::RNonHomogeneousTreeLikelihood::computeTreeDLikelihood(), bpp::RNonHomogeneousTreeLikelihood::computeTreeDLikelihood(), bpp::RNonHomogeneousTreeLikelihood::computeTreeDLikelihood(), bpp::RNonHomogeneousTreeLikelihood::computeTreeDLikelihood(), bpp::RNonHomogeneousTreeLikelihood::computeTreeDLikelihood(), bpp::RNonHomogeneousTreeLikelihood::computeTreeDLikelihood(), bpp::RNonHomogeneousTreeLikelihood::computeTreeDLikelihood(), bpp::RNonHomogeneousTreeLikelihood::computeTreeDLikelihood(), bpp::RNonHomogeneousTreeLikelihood::computeTreeDLikelihood(), bpp::RNonHomogeneousTreeLikelihood::computeTreeDLikelihood(), bpp::RNonHomogeneousTreeLikelihood::computeTreeDLikelihood(), bpp::RNonHomogeneousTreeLikelihood::computeTreeDLikelihood(), bpp::RNonHomogeneousTreeLikelihood::computeTreeDLikelihood(), bpp::RNonHomogeneousTreeLikelihood::computeTreeDLikelihood(), bpp::RNonHomogeneousTreeLikelihood::computeTreeDLikelihood(), bpp::RNonHomogeneousTreeLikelihood::computeTreeDLikelihood(), bpp::RNonHomogeneousTreeLikelihood::computeTreeDLikelihood(), bpp::RNonHomogeneousTreeLikelihood::computeTreeDLikelihood(), bpp::RNonHomogeneousTreeLikelihood::computeTreeDLikelihood(), bpp::RNonHomogeneousTreeLikelihood::computeTreeDLikelihood(), bpp::RNonHomogeneousTreeLikelihood::computeTreeDLikelihood(), bpp::RNonHomogeneousTreeLikelihood::computeTreeDLikelihood(), bpp::RNonHomogeneousTreeLikelihood::computeTreeDLikelihood(), bpp::RNonHomogeneousTreeLikelihood::computeTreeDLikelihood(), bpp::RNonHomogeneousTreeLikelihood::computeTreeDLikelihood(), bpp::RNonHomogeneousTreeLikelihood::computeTreeDLikelihood(), bpp::RNonHomogeneousTreeLikelihood::computeTreeDLikelihood(), bpp::RNonHomogeneousMixedTreeLikelihood::computeTreeDLikelihood(), bpp::RNonHomogeneousMixedTreeLikelihood::computeTreeDLikelihood(), bpp::RNonHomogeneousMixedTreeLikelihood::computeTreeDLikelihood(), bpp::DRHomogeneousTreeLikelihood::computeTreeDLikelihoodAtNode(), bpp::DRHomogeneousTreeLikelihood::computeTreeDLikelihoodAtNode(), bpp::DRHomogeneousTreeLikelihood::computeTreeDLikelihoodAtNode(), bpp::DRHomogeneousTreeLikelihood::computeTreeDLikelihoodAtNode(), bpp::DRHomogeneousTreeLikelihood::computeTreeDLikelihoodAtNode(), bpp::DRNonHomogeneousTreeLikelihood::computeTreeDLikelihoodAtNode(), bpp::DRNonHomogeneousTreeLikelihood::computeTreeDLikelihoodAtNode(), bpp::DRNonHomogeneousTreeLikelihood::computeTreeDLikelihoodAtNode(), bpp::DRNonHomogeneousTreeLikelihood::computeTreeDLikelihoodAtNode(), bpp::DRNonHomogeneousTreeLikelihood::computeTreeDLikelihoodAtNode(), bpp::NonHomogeneousSequenceSimulator::dEvolveInternal(), bpp::DRHomogeneousTreeLikelihood::displayLikelihood(), bpp::DRHomogeneousTreeLikelihood::displayLikelihood(), bpp::DRHomogeneousTreeLikelihood::displayLikelihood(), bpp::DRHomogeneousTreeLikelihood::displayLikelihood(), bpp::DRHomogeneousTreeLikelihood::displayLikelihood(), bpp::DRHomogeneousTreeLikelihood::displayLikelihood(), bpp::DRHomogeneousTreeLikelihood::displayLikelihood(), bpp::DRNonHomogeneousTreeLikelihood::displayLikelihood(), bpp::DRNonHomogeneousTreeLikelihood::displayLikelihood(), bpp::DRNonHomogeneousTreeLikelihood::displayLikelihood(), bpp::DRNonHomogeneousTreeLikelihood::displayLikelihood(), bpp::DRNonHomogeneousTreeLikelihood::displayLikelihood(), bpp::DRNonHomogeneousTreeLikelihood::displayLikelihood(), bpp::DRNonHomogeneousTreeLikelihood::displayLikelihood(), bpp::RHomogeneousTreeLikelihood::displayLikelihood(), bpp::RNonHomogeneousTreeLikelihood::displayLikelihood(), bpp::NNIHomogeneousTreeLikelihood::doNNI(), bpp::TreeTemplateTools::getAncestorsId(), bpp::TreeTemplateTools::getBranchProperties(), bpp::TreeTemplateTools::getBranchProperties(), getFatherId(), bpp::TreeTemplateTools::getInnerNodesId(), bpp::TreeTemplateTools::getLeavesId(), bpp::AbstractTreeDrawing::getNodeAt(), bpp::AbstractTreeDrawing::getNodePosition(), bpp::TreeTemplateTools::getNodeProperties(), bpp::TreeTemplateTools::getNodeProperties(), bpp::TreeTemplateTools::getNodesId(), bpp::DRNonHomogeneousTreeLikelihood::getSecondOrderDerivative(), bpp::DRNonHomogeneousTreeLikelihood::getSecondOrderDerivative(), bpp::DRNonHomogeneousTreeLikelihood::getSecondOrderDerivative(), bpp::DRNonHomogeneousTreeLikelihood::getSecondOrderDerivative(), bpp::DRNonHomogeneousTreeLikelihood::getSecondOrderDerivative(), bpp::DRNonHomogeneousTreeLikelihood::getSecondOrderDerivative(), bpp::DRNonHomogeneousTreeLikelihood::getSecondOrderDerivative(), bpp::DRNonHomogeneousTreeLikelihood::getSecondOrderDerivative(), bpp::DRNonHomogeneousTreeLikelihood::getSecondOrderDerivative(), bpp::DRNonHomogeneousTreeLikelihood::getSecondOrderDerivative(), bpp::DRNonHomogeneousTreeLikelihood::getSecondOrderDerivative(), bpp::DRNonHomogeneousTreeLikelihood::getSecondOrderDerivative(), bpp::DRNonHomogeneousTreeLikelihood::getSecondOrderDerivative(), bpp::DRNonHomogeneousTreeLikelihood::getSecondOrderDerivative(), bpp::TreeTemplateTools::incrementAllIds(), bpp::NonHomogeneousSequenceSimulator::init(), bpp::DRTreeParsimonyData::init(), bpp::DRTreeParsimonyData::init(), bpp::AbstractNonHomogeneousTreeLikelihood::init_(), bpp::DRASRTreeLikelihoodData::initLikelihoods(), bpp::DRASDRTreeLikelihoodData::initLikelihoods(), bpp::DRASDRTreeLikelihoodData::initLikelihoods(), bpp::DRASRTreeLikelihoodData::initLikelihoodsWithPatterns(), bpp::TreeTemplateTools::nodeToParenthesis(), bpp::AbstractNonHomogeneousTreeLikelihood::operator=(), bpp::Nhx::propertiesToParenthesis(), bpp::MarginalAncestralStateReconstruction::recursiveMarginalAncestralStates(), bpp::MarginalAncestralStateReconstruction::recursiveMarginalAncestralStates(), bpp::MarginalAncestralStateReconstruction::recursiveMarginalAncestralStates(), bpp::DRTreeParsimonyData::reInit(), bpp::DRTreeParsimonyData::reInit(), bpp::DRASDRTreeLikelihoodData::reInit(), bpp::DRHomogeneousTreeLikelihood::resetLikelihoodArrays(), bpp::DRHomogeneousTreeLikelihood::resetLikelihoodArrays(), bpp::DRHomogeneousTreeLikelihood::resetLikelihoodArrays(), bpp::DRHomogeneousTreeLikelihood::resetLikelihoodArrays(), bpp::DRNonHomogeneousTreeLikelihood::resetLikelihoodArrays(), bpp::DRNonHomogeneousTreeLikelihood::resetLikelihoodArrays(), bpp::DRNonHomogeneousTreeLikelihood::resetLikelihoodArrays(), bpp::DRNonHomogeneousTreeLikelihood::resetLikelihoodArrays(), bpp::NNITopologySearch::searchBetter(), bpp::NNITopologySearch::searchBetter(), bpp::NNITopologySearch::searchBetter(), bpp::NNITopologySearch::searchBetter(), bpp::NNITopologySearch::searchBetter(), bpp::NNITopologySearch::searchBetter(), bpp::NNITopologySearch::searchFast(), bpp::NNITopologySearch::searchFast(), bpp::NNITopologySearch::searchFast(), bpp::NNITopologySearch::searchFast(), bpp::NNITopologySearch::searchFast(), bpp::NNITopologySearch::searchFast(), bpp::TreeTemplateTools::searchFirstNodeWithId(), bpp::TreeTemplateTools::searchFirstNodeWithId(), bpp::NNITopologySearch::searchPhyML(), bpp::NNITopologySearch::searchPhyML(), bpp::NNITopologySearch::searchPhyML(), bpp::NNITopologySearch::searchPhyML(), bpp::NNITopologySearch::searchPhyML(), bpp::NNITopologySearch::searchPhyML(), bpp::NNITopologySearch::searchPhyML(), bpp::NNITopologySearch::searchPhyML(), bpp::NNITopologySearch::searchPhyML(), bpp::NNITopologySearch::searchPhyML(), bpp::NNITopologySearch::searchPhyML(), bpp::NNITopologySearch::searchPhyML(), bpp::NNITopologySearch::searchPhyML(), bpp::AbstractHomogeneousTreeLikelihood::setSubstitutionModel(), bpp::AbstractHomogeneousTreeLikelihood::setSubstitutionModel(), bpp::AbstractHomogeneousTreeLikelihood::setSubstitutionModel(), bpp::AbstractNonHomogeneousTreeLikelihood::setSubstitutionModelSet(), bpp::AbstractNonHomogeneousTreeLikelihood::setSubstitutionModelSet(), bpp::AbstractNonHomogeneousTreeLikelihood::setSubstitutionModelSet(), bpp::DRTreeParsimonyScore::testNNI(), bpp::DRTreeParsimonyScore::testNNI(), bpp::DRTreeParsimonyScore::testNNI(), bpp::DRTreeParsimonyScore::testNNI(), bpp::DRTreeParsimonyScore::testNNI(), bpp::DRTreeParsimonyScore::testNNI(), bpp::DRTreeParsimonyScore::testNNI(), bpp::DRTreeParsimonyScore::testNNI(), bpp::DRTreeParsimonyScore::testNNI(), bpp::DRTreeParsimonyScore::testNNI(), bpp::NNIHomogeneousTreeLikelihood::testNNI(), bpp::NNIHomogeneousTreeLikelihood::testNNI(), bpp::NNIHomogeneousTreeLikelihood::testNNI(), bpp::NNIHomogeneousTreeLikelihood::testNNI(), bpp::NNIHomogeneousTreeLikelihood::testNNI(), bpp::NNIHomogeneousTreeLikelihood::testNNI(), bpp::NNIHomogeneousTreeLikelihood::testNNI(), bpp::NNIHomogeneousTreeLikelihood::testNNI(), bpp::NNIHomogeneousTreeLikelihood::testNNI(), bpp::NNIHomogeneousTreeLikelihood::testNNI(), bpp::NNIHomogeneousTreeLikelihood::testNNI(), bpp::NNIHomogeneousTreeLikelihood::testNNI(), and bpp::NNIHomogeneousTreeLikelihood::testNNI().

virtual std::string bpp::Node::getName ( ) const throw (NodePException)

inlinevirtual

Get the name associated to this node, if there is one, otherwise throw a NodeException.

Returns

The name associated to this node.

Definition at line 235 of file Node.h.

References hasName(), and name_.

Referenced by bpp::LeafNamesTreeDrawingListener::afterDrawNode(), bpp::LabelInnerNodesTreeDrawingListener::afterDrawNode(), bpp::LabelCollapsedNodesTreeDrawingListener::afterDrawNode(), bpp::BipartitionList::buildBitBipartitions(), bpp::RHomogeneousTreeLikelihood::displayLikelihood(), bpp::RNonHomogeneousTreeLikelihood::displayLikelihood(), bpp::TreeTemplateTools::getLeavesNames(), bpp::TreeTemplateTools::haveSameOrderedTopology(), bpp::TreeTemplateTools::haveSameOrderedTopology(), bpp::Nhx::nodeToParenthesis(), bpp::TreeTemplateTools::nodeToParenthesis(), bpp::TreeTemplateTools::nodeToParenthesis(), bpp::TreeTemplateTools::orderTree_(), bpp::TreeTemplateTools::processDistsInSubtree_(), bpp::TreeTemplateTools::processDistsInSubtree_(), bpp::MarginalAncestralStateReconstruction::recursiveMarginalAncestralStates(), bpp::Nhx::treeToParenthesis(), bpp::TreeTemplateTools::treeToParenthesis(), and bpp::TreeTemplateTools::treeToParenthesis().

vector< const Node * > Node::getNeighbors

(

)

const

Definition at line 114 of file Node.cpp.

References father_, hasFather(), sons_, and sons_.

Referenced by bpp::DRTreeParsimonyScore::computeScoresForNode(), bpp::DRTreeParsimonyScore::computeScoresPostorderForNode(), bpp::DRTreeParsimonyScore::computeScoresPreorderForNode(), bpp::NodeTemplate< NodeInfos >::getNeighbors(), bpp::NodeTemplate< NodeInfos >::getNeighbors(), and bpp::TreeTemplateTools::getRemainingNeighbors().

vector< Node * > Node::getNeighbors

(

)

Definition at line 122 of file Node.cpp.

References father_, hasFather(), sons_, and sons_.

virtual Clonable* bpp::Node::getNodeProperty ( const std::string &  name ) throw (PropertyNotFoundException)

inlinevirtual

Definition at line 526 of file Node.h.

References hasNodeProperty(), and nodeProperties_.

Referenced by bpp::Nhx::changeNamesToTags(), bpp::Nhx::changeTagsToNames(), bpp::TreeTemplateTools::getNodeProperties(), bpp::TreeTemplateTools::getNodeProperties(), and bpp::Nhx::propertiesToParenthesis().

virtual const Clonable* bpp::Node::getNodeProperty ( const std::string &  name ) const throw (PropertyNotFoundException)

inlinevirtual

Definition at line 534 of file Node.h.

References hasNodeProperty(), and nodeProperties_.

virtual std::vector<std::string> bpp::Node::getNodePropertyNames ( ) const

inlinevirtual

Definition at line 589 of file Node.h.

References bpp::MapTools::getKeys().

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

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

inlinevirtual

Definition at line 387 of file Node.h.

References sons_.

Referenced by bpp::BipartitionList::buildBitBipartitions(), bpp::BipartitionList::buildBitBipartitions(), bpp::BipartitionList::buildBitBipartitions(), bpp::Nhx::changeNamesToTags(), bpp::Nhx::changeTagsToNames(), bpp::TreeTemplateTools::cloneSubtree(), bpp::RHomogeneousTreeLikelihood::computeDownSubtreeD2Likelihood(), bpp::RNonHomogeneousTreeLikelihood::computeDownSubtreeD2Likelihood(), bpp::RHomogeneousTreeLikelihood::computeDownSubtreeDLikelihood(), bpp::RNonHomogeneousTreeLikelihood::computeDownSubtreeDLikelihood(), bpp::PhyloStatistics::computeForSubtree_(), bpp::PhyloStatistics::computeForSubtree_(), bpp::DRHomogeneousTreeLikelihood::computeLikelihoodAtNode_(), bpp::DRNonHomogeneousTreeLikelihood::computeLikelihoodAtNode_(), bpp::DRHomogeneousTreeLikelihood::computeRootLikelihood(), bpp::DRNonHomogeneousTreeLikelihood::computeRootLikelihood(), bpp::DRTreeParsimonyScore::computeScoresPostorder(), bpp::DRTreeParsimonyScore::computeScoresPreorder(), bpp::DRTreeParsimonyScore::computeScoresPreorder(), bpp::SubstitutionMappingTools::computeSubstitutionVectors(), bpp::SubstitutionMappingTools::computeSubstitutionVectorsNoAveraging(), bpp::RHomogeneousTreeLikelihood::computeSubtreeLikelihood(), bpp::RNonHomogeneousTreeLikelihood::computeSubtreeLikelihood(), bpp::DRHomogeneousTreeLikelihood::computeSubtreeLikelihoodPostfix(), bpp::DRHomogeneousTreeLikelihood::computeSubtreeLikelihoodPostfix(), bpp::DRHomogeneousTreeLikelihood::computeSubtreeLikelihoodPostfix(), bpp::DRNonHomogeneousTreeLikelihood::computeSubtreeLikelihoodPostfix(), bpp::DRNonHomogeneousTreeLikelihood::computeSubtreeLikelihoodPostfix(), bpp::DRNonHomogeneousTreeLikelihood::computeSubtreeLikelihoodPostfix(), bpp::DRHomogeneousTreeLikelihood::computeSubtreeLikelihoodPrefix(), bpp::DRHomogeneousTreeLikelihood::computeSubtreeLikelihoodPrefix(), bpp::DRHomogeneousTreeLikelihood::computeSubtreeLikelihoodPrefix(), bpp::DRNonHomogeneousTreeLikelihood::computeSubtreeLikelihoodPrefix(), bpp::DRNonHomogeneousTreeLikelihood::computeSubtreeLikelihoodPrefix(), bpp::DRNonHomogeneousTreeLikelihood::computeSubtreeLikelihoodPrefix(), bpp::RHomogeneousTreeLikelihood::computeTreeD2Likelihood(), bpp::RNonHomogeneousTreeLikelihood::computeTreeD2Likelihood(), bpp::RNonHomogeneousTreeLikelihood::computeTreeD2Likelihood(), bpp::RNonHomogeneousTreeLikelihood::computeTreeD2Likelihood(), bpp::RHomogeneousTreeLikelihood::computeTreeDLikelihood(), bpp::RNonHomogeneousTreeLikelihood::computeTreeDLikelihood(), bpp::RNonHomogeneousTreeLikelihood::computeTreeDLikelihood(), bpp::RNonHomogeneousTreeLikelihood::computeTreeDLikelihood(), degree(), bpp::TreeTemplateTools::deleteBranchLengths(), bpp::NonHomogeneousSequenceSimulator::dEvolve(), bpp::NonHomogeneousSequenceSimulator::dEvolveInternal(), bpp::DRHomogeneousTreeLikelihood::displayLikelihood(), bpp::DRNonHomogeneousTreeLikelihood::displayLikelihood(), bpp::NonHomogeneousSequenceSimulator::evolveInternal(), bpp::NonHomogeneousSequenceSimulator::evolveInternal(), bpp::TreeTemplateTools::getBranchesId(), bpp::TreeTemplateTools::getBranchProperties(), bpp::TreeTemplateTools::getBranchProperties(), bpp::TreeTemplateTools::getBranchPropertyNames(), bpp::TreeTemplateTools::getDepth(), bpp::TreeTemplateTools::getDepths(), bpp::TreeTemplateTools::getHeight(), bpp::TreeTemplateTools::getHeights(), bpp::TreeTemplateTools::getInnerNodesId(), bpp::TreeTemplateTools::getLeavesId(), bpp::TreeTemplateTools::getLeavesNames(), bpp::TreeTemplateTools::getNodeProperties(), bpp::TreeTemplateTools::getNodeProperties(), bpp::TreeTemplateTools::getNodePropertyNames(), bpp::TreeTemplateTools::getNodesId(), bpp::TreeTemplateTools::getNumberOfLeaves(), bpp::TreeTemplateTools::getNumberOfNodes(), bpp::DRNonHomogeneousTreeLikelihood::getSecondOrderDerivative(), bpp::DRNonHomogeneousTreeLikelihood::getSecondOrderDerivative(), bpp::TreeTemplateTools::getSubtreeMoments(), bpp::TreeTemplateTools::haveSameOrderedTopology(), bpp::TreeTemplateTools::haveSameOrderedTopology(), bpp::TreeTemplateTools::haveSameOrderedTopology(), bpp::TreeTemplateTools::incrementAllIds(), bpp::TreeTemplateTools::isMultifurcating(), bpp::TreeTemplateTools::isMultifurcating(), bpp::NonHomogeneousSequenceSimulator::multipleEvolve(), bpp::NonHomogeneousSequenceSimulator::multipleEvolveInternal(), bpp::Nhx::nodeToParenthesis(), bpp::TreeTemplateTools::nodeToParenthesis(), bpp::TreeTemplateTools::nodeToParenthesis(), bpp::TreeTemplateTools::orderTree_(), bpp::TreeTemplateTools::processDistsInSubtree_(), bpp::TreeTemplateTools::processDistsInSubtree_(), bpp::TreeTemplateTools::processDistsInSubtree_(), bpp::MarginalAncestralStateReconstruction::recursiveMarginalAncestralStates(), bpp::PhylogramPlot::recursivePlot_(), bpp::CladogramPlot::recursivePlot_(), bpp::DRHomogeneousTreeLikelihood::resetLikelihoodArrays(), bpp::DRNonHomogeneousTreeLikelihood::resetLikelihoodArrays(), bpp::TreeTemplateTools::searchFirstNodeWithId(), bpp::TreeTemplateTools::searchFirstNodeWithId(), bpp::TreeTemplateTools::setBranchLengths(), bpp::TreeTemplateTools::setVoidBranchLengths(), bpp::NonHomogeneousSequenceSimulator::simulate(), bpp::NonHomogeneousSequenceSimulator::simulate(), bpp::Nhx::treeToParenthesis(), bpp::Nhx::treeToParenthesis(), bpp::TreeTemplateTools::treeToParenthesis(), bpp::TreeTemplateTools::treeToParenthesis(), bpp::TreeTemplateTools::treeToParenthesis(), and bpp::TreeTemplateTools::treeToParenthesis().

virtual const Node* bpp::Node::getSon ( size_t  pos ) const throw (IndexOutOfBoundsException)

inlinevirtual

Reimplemented in bpp::NodeTemplate< NodeInfos >.

Definition at line 394 of file Node.h.

References sons_, sons_, and sons_.

Referenced by bpp::BipartitionList::buildBitBipartitions(), bpp::BipartitionList::buildBitBipartitions(), bpp::Nhx::changeNamesToTags(), bpp::Nhx::changeTagsToNames(), bpp::RHomogeneousClockTreeLikelihood::computeBranchLengthsFromHeights(), bpp::GlobalClockTreeLikelihoodFunctionWrapper::computeBranchLengthsFromHeights_(), bpp::RHomogeneousTreeLikelihood::computeDownSubtreeD2Likelihood(), bpp::RNonHomogeneousTreeLikelihood::computeDownSubtreeD2Likelihood(), bpp::RHomogeneousTreeLikelihood::computeDownSubtreeDLikelihood(), bpp::RNonHomogeneousTreeLikelihood::computeDownSubtreeDLikelihood(), bpp::DRHomogeneousTreeLikelihood::computeLikelihoodAtNode_(), bpp::DRNonHomogeneousTreeLikelihood::computeLikelihoodAtNode_(), bpp::DRHomogeneousTreeLikelihood::computeRootLikelihood(), bpp::DRNonHomogeneousTreeLikelihood::computeRootLikelihood(), bpp::DRTreeParsimonyScore::computeScoresPostorder(), bpp::DRTreeParsimonyScore::computeScoresPreorder(), bpp::SubstitutionMappingTools::computeSubstitutionVectors(), bpp::SubstitutionMappingTools::computeSubstitutionVectorsNoAveraging(), bpp::RHomogeneousTreeLikelihood::computeSubtreeLikelihood(), bpp::RNonHomogeneousTreeLikelihood::computeSubtreeLikelihood(), bpp::DRHomogeneousTreeLikelihood::computeSubtreeLikelihoodPostfix(), bpp::DRHomogeneousTreeLikelihood::computeSubtreeLikelihoodPostfix(), bpp::DRNonHomogeneousTreeLikelihood::computeSubtreeLikelihoodPostfix(), bpp::DRNonHomogeneousTreeLikelihood::computeSubtreeLikelihoodPostfix(), bpp::DRHomogeneousTreeLikelihood::computeSubtreeLikelihoodPrefix(), bpp::DRHomogeneousTreeLikelihood::computeSubtreeLikelihoodPrefix(), bpp::DRHomogeneousTreeLikelihood::computeSubtreeLikelihoodPrefix(), bpp::DRNonHomogeneousTreeLikelihood::computeSubtreeLikelihoodPrefix(), bpp::DRNonHomogeneousTreeLikelihood::computeSubtreeLikelihoodPrefix(), bpp::DRNonHomogeneousTreeLikelihood::computeSubtreeLikelihoodPrefix(), bpp::RHomogeneousTreeLikelihood::computeTreeD2Likelihood(), bpp::RNonHomogeneousTreeLikelihood::computeTreeD2Likelihood(), bpp::RNonHomogeneousTreeLikelihood::computeTreeD2Likelihood(), bpp::RNonHomogeneousTreeLikelihood::computeTreeD2Likelihood(), bpp::RNonHomogeneousTreeLikelihood::computeTreeD2Likelihood(), bpp::RNonHomogeneousTreeLikelihood::computeTreeD2Likelihood(), bpp::RNonHomogeneousTreeLikelihood::computeTreeD2Likelihood(), bpp::RNonHomogeneousTreeLikelihood::computeTreeD2Likelihood(), bpp::RHomogeneousTreeLikelihood::computeTreeDLikelihood(), bpp::RNonHomogeneousTreeLikelihood::computeTreeDLikelihood(), bpp::RNonHomogeneousTreeLikelihood::computeTreeDLikelihood(), bpp::RNonHomogeneousTreeLikelihood::computeTreeDLikelihood(), bpp::RNonHomogeneousTreeLikelihood::computeTreeDLikelihood(), bpp::RNonHomogeneousTreeLikelihood::computeTreeDLikelihood(), bpp::RNonHomogeneousTreeLikelihood::computeTreeDLikelihood(), bpp::RNonHomogeneousTreeLikelihood::computeTreeDLikelihood(), bpp::TreeTemplateTools::deleteBranchLengths(), bpp::DRHomogeneousTreeLikelihood::displayLikelihood(), bpp::DRNonHomogeneousTreeLikelihood::displayLikelihood(), bpp::DRTreeParsimonyScore::doNNI(), bpp::NNIHomogeneousTreeLikelihood::doNNI(), bpp::TreeTemplateTools::getBranchesId(), bpp::TreeTemplateTools::getBranchProperties(), bpp::TreeTemplateTools::getBranchProperties(), bpp::TreeTemplateTools::getBranchPropertyNames(), bpp::TreeTemplateTools::getInnerNodesId(), bpp::TreeTemplateTools::getLeavesId(), bpp::TreeTemplateTools::getLeavesNames(), bpp::TreeTemplateTools::getNodeProperties(), bpp::TreeTemplateTools::getNodeProperties(), bpp::TreeTemplateTools::getNodePropertyNames(), bpp::TreeTemplateTools::getNodesId(), bpp::DRNonHomogeneousTreeLikelihood::getSecondOrderDerivative(), bpp::DRNonHomogeneousTreeLikelihood::getSecondOrderDerivative(), bpp::TreeTemplateTools::getSubtreeMoments(), bpp::TreeTemplateTools::haveSameOrderedTopology(), bpp::TreeTemplateTools::haveSameOrderedTopology(), bpp::TreeTemplateTools::incrementAllIds(), bpp::TreeTemplateTools::isMultifurcating(), bpp::TreeTemplateTools::orderTree_(), bpp::TreeTemplateTools::processDistsInSubtree_(), bpp::TreeTemplateTools::processDistsInSubtree_(), bpp::TreeTemplateTools::processDistsInSubtree_(), bpp::TreeTemplateTools::processDistsInSubtree_(), bpp::TreeTemplateTools::processDistsInSubtree_(), bpp::MarginalAncestralStateReconstruction::recursiveMarginalAncestralStates(), bpp::DRHomogeneousTreeLikelihood::resetLikelihoodArrays(), bpp::DRNonHomogeneousTreeLikelihood::resetLikelihoodArrays(), bpp::TreeTemplateTools::searchFirstNodeWithId(), bpp::TreeTemplateTools::searchFirstNodeWithId(), bpp::TreeTemplateTools::setBranchLengths(), bpp::TreeTemplateTools::setVoidBranchLengths(), bpp::DRTreeParsimonyScore::testNNI(), bpp::NNIHomogeneousTreeLikelihood::testNNI(), bpp::Nhx::treeToParenthesis(), bpp::Nhx::treeToParenthesis(), bpp::Nhx::treeToParenthesis(), bpp::TreeTemplateTools::treeToParenthesis(), bpp::TreeTemplateTools::treeToParenthesis(), bpp::TreeTemplateTools::treeToParenthesis(), bpp::TreeTemplateTools::treeToParenthesis(), bpp::TreeTemplateTools::treeToParenthesis(), and bpp::TreeTemplateTools::treeToParenthesis().

virtual Node* bpp::Node::getSon ( size_t  pos ) throw (IndexOutOfBoundsException)

inlinevirtual

Reimplemented in bpp::NodeTemplate< NodeInfos >.

Definition at line 400 of file Node.h.

References sons_, sons_, and sons_.

size_t Node::getSonPosition ( const Node *  son ) const throw (NodeNotFoundException, NullPointerException)

virtual

Definition at line 130 of file Node.cpp.

References bpp::TextTools::toString().

Referenced by bpp::DRTreeParsimonyScore::doNNI(), bpp::NNIHomogeneousTreeLikelihood::doNNI(), bpp::DRTreeParsimonyScore::testNNI(), and bpp::NNIHomogeneousTreeLikelihood::testNNI().

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

inlinevirtual

Definition at line 389 of file Node.h.

References sons_.

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

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

inlinevirtual

Definition at line 211 of file Node.h.

References sons_, sons_, and sons_.

bool Node::hasBootstrapValue ( ) const

virtual

Definition at line 141 of file Node.cpp.

References hasBranchProperty().

virtual bool bpp::Node::hasBranchProperty ( const std::string &  name ) const

inlinevirtual

Definition at line 677 of file Node.h.

References branchProperties_, and branchProperties_.

Referenced by bpp::BootstrapValuesTreeDrawingListener::afterDrawBranch(), bpp::Nhx::changeNamesToTags(), bpp::Nhx::changeTagsToNames(), deleteBranchProperty(), getBootstrapValue(), bpp::TreeTemplateTools::getBranchProperties(), bpp::TreeTemplateTools::getBranchProperties(), getBranchProperty(), getBranchProperty(), hasBootstrapValue(), bpp::TreeTemplateTools::nodeToParenthesis(), bpp::TreeTemplateTools::nodeToParenthesis(), bpp::TreeTemplateTools::nodeToParenthesis(), bpp::Nhx::propertiesToParenthesis(), removeBranchProperty(), setBranchProperty(), bpp::TreeTemplateTools::treeToParenthesis(), and bpp::TreeTemplateTools::treeToParenthesis().

virtual bool bpp::Node::hasDistanceToFather ( ) const

inlinevirtual

Tell is this node has a distance to the father.

Returns

True if distanceToFather != 0.

Definition at line 320 of file Node.h.

References distanceToFather_.

Referenced by bpp::BranchLengthsTreeDrawingListener::afterDrawBranch(), bpp::PhyloStatistics::computeForSubtree_(), bpp::PhyloStatistics::computeForSubtree_(), getDistanceToFather(), Node(), bpp::Nhx::nodeToParenthesis(), bpp::TreeTemplateTools::nodeToParenthesis(), bpp::TreeTemplateTools::nodeToParenthesis(), operator=(), bpp::PhylogramPlot::recursivePlot_(), bpp::PhylogramPlot::recursivePlot_(), bpp::TreeTemplateTools::setVoidBranchLengths(), bpp::Nhx::treeToParenthesis(), and bpp::TreeTemplateTools::treeToParenthesis().

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

inlinevirtual

Tell if this node has a father node.

Definition at line 378 of file Node.h.

References father_.

Referenced by bpp::BipartitionList::buildBitBipartitions(), bpp::BipartitionList::buildBitBipartitions(), bpp::DRHomogeneousTreeLikelihood::computeLikelihoodAtNode_(), bpp::DRNonHomogeneousTreeLikelihood::computeLikelihoodAtNode_(), bpp::DRTreeParsimonyScore::computeScoresPreorder(), bpp::SubstitutionMappingTools::computeSubstitutionVectors(), bpp::SubstitutionMappingTools::computeSubstitutionVectorsNoAveraging(), bpp::DRHomogeneousTreeLikelihood::computeSubtreeLikelihoodPrefix(), bpp::DRHomogeneousTreeLikelihood::computeSubtreeLikelihoodPrefix(), bpp::DRHomogeneousTreeLikelihood::computeSubtreeLikelihoodPrefix(), bpp::DRNonHomogeneousTreeLikelihood::computeSubtreeLikelihoodPrefix(), bpp::DRNonHomogeneousTreeLikelihood::computeSubtreeLikelihoodPrefix(), bpp::DRNonHomogeneousTreeLikelihood::computeSubtreeLikelihoodPrefix(), degree(), bpp::NonHomogeneousSequenceSimulator::dEvolveInternal(), bpp::DRHomogeneousTreeLikelihood::displayLikelihood(), bpp::DRNonHomogeneousTreeLikelihood::displayLikelihood(), bpp::DRTreeParsimonyScore::doNNI(), bpp::DRTreeParsimonyScore::doNNI(), bpp::NNIHomogeneousTreeLikelihood::doNNI(), bpp::NNIHomogeneousTreeLikelihood::doNNI(), bpp::AbstractTreeDrawing::drawAtBranch(), bpp::NonHomogeneousSequenceSimulator::evolveInternal(), bpp::NonHomogeneousSequenceSimulator::evolveInternal(), bpp::TreeTemplateTools::getAncestorsId(), getNeighbors(), getNeighbors(), bpp::TreeTemplateTools::getPathBetweenAnyTwoNodes(), bpp::TreeTemplateTools::getPathBetweenAnyTwoNodes(), bpp::TreeTemplateTools::getPathBetweenAnyTwoNodes(), bpp::TreeTemplateTools::getPathBetweenAnyTwoNodes(), bpp::TreeTemplateTools::isRoot(), bpp::NonHomogeneousSequenceSimulator::multipleEvolveInternal(), bpp::TreeTemplateTools::orderTree_(), bpp::TreeTemplateTools::processDistsInSubtree_(), bpp::DRHomogeneousTreeLikelihood::resetLikelihoodArrays(), bpp::DRNonHomogeneousTreeLikelihood::resetLikelihoodArrays(), bpp::DRTreeParsimonyScore::testNNI(), bpp::DRTreeParsimonyScore::testNNI(), bpp::NNIHomogeneousTreeLikelihood::testNNI(), bpp::NNIHomogeneousTreeLikelihood::testNNI(), and bpp::NNIHomogeneousTreeLikelihood::testNNI().

virtual bool bpp::Node::hasName ( ) const

inlinevirtual

Tell is this node has a name.

Returns

True if name != 0.

Definition at line 266 of file Node.h.

References name_.

Referenced by bpp::LabelInnerNodesTreeDrawingListener::afterDrawNode(), bpp::LabelCollapsedNodesTreeDrawingListener::afterDrawNode(), getName(), Node(), operator=(), and bpp::TreeTemplateTools::treeToParenthesis().

virtual bool bpp::Node::hasNodeProperty ( const std::string &  name ) const

inlinevirtual

Definition at line 587 of file Node.h.

References nodeProperties_, and nodeProperties_.

Referenced by bpp::Nhx::changeNamesToTags(), bpp::Nhx::changeTagsToNames(), deleteNodeProperty(), bpp::TreeTemplateTools::getNodeProperties(), bpp::TreeTemplateTools::getNodeProperties(), getNodeProperty(), getNodeProperty(), bpp::Nhx::propertiesToParenthesis(), bpp::Nhx::propertiesToParenthesis(), removeNodeProperty(), and setNodeProperty().

virtual bool bpp::Node::isLeaf ( ) const

inlinevirtual

Definition at line 691 of file Node.h.

References degree().

Referenced by bpp::LeafNamesTreeDrawingListener::afterDrawNode(), bpp::RHomogeneousClockTreeLikelihood::computeBranchLengthsFromHeights(), bpp::GlobalClockTreeLikelihoodFunctionWrapper::computeBranchLengthsFromHeights_(), bpp::PhyloStatistics::computeForSubtree_(), bpp::DRHomogeneousTreeLikelihood::computeLikelihoodAtNode_(), bpp::DRNonHomogeneousTreeLikelihood::computeLikelihoodAtNode_(), bpp::DRHomogeneousTreeLikelihood::computeRootLikelihood(), bpp::DRNonHomogeneousTreeLikelihood::computeRootLikelihood(), bpp::DRTreeParsimonyScore::computeScoresPostorder(), bpp::DRTreeParsimonyScore::computeScoresPostorder(), bpp::DRTreeParsimonyScore::computeScoresPreorder(), bpp::RHomogeneousTreeLikelihood::computeSubtreeLikelihood(), bpp::RNonHomogeneousTreeLikelihood::computeSubtreeLikelihood(), bpp::RNonHomogeneousMixedTreeLikelihood::computeSubtreeLikelihood(), bpp::DRHomogeneousTreeLikelihood::computeSubtreeLikelihoodPostfix(), bpp::DRNonHomogeneousTreeLikelihood::computeSubtreeLikelihoodPostfix(), bpp::DRHomogeneousTreeLikelihood::computeSubtreeLikelihoodPrefix(), bpp::DRHomogeneousTreeLikelihood::computeSubtreeLikelihoodPrefix(), bpp::DRNonHomogeneousTreeLikelihood::computeSubtreeLikelihoodPrefix(), bpp::DRNonHomogeneousTreeLikelihood::computeSubtreeLikelihoodPrefix(), bpp::TreeTemplateTools::getInnerNodesId(), bpp::TreeTemplateTools::getLeavesId(), bpp::TreeTemplateTools::getLeavesNames(), bpp::TreeTemplateTools::getNumberOfLeaves(), bpp::TreeTemplateTools::getSubtreeMoments(), bpp::TreeTemplateTools::haveSameOrderedTopology(), bpp::TreeTemplateTools::haveSameOrderedTopology(), bpp::DRASDRTreeLikelihoodData::initLikelihoods(), bpp::Nhx::nodeToParenthesis(), bpp::TreeTemplateTools::nodeToParenthesis(), bpp::TreeTemplateTools::nodeToParenthesis(), bpp::TreeTemplateTools::nodeToParenthesis(), bpp::TreeTemplateTools::orderTree_(), bpp::TreeTemplateTools::processDistsInSubtree_(), bpp::MarginalAncestralStateReconstruction::recursiveMarginalAncestralStates(), bpp::PhylogramPlot::recursivePlot_(), bpp::CladogramPlot::recursivePlot_(), bpp::Nhx::treeToParenthesis(), bpp::TreeTemplateTools::treeToParenthesis(), and bpp::TreeTemplateTools::treeToParenthesis().

Node & Node::operator=

(

const Node &

node

)

Assignation operator.

Warning

This operator copies all fields, excepted father and son node pointers.

Parameters

node	the node to copy.

Returns

A reference toward this node.

Assignation operator:

Definition at line 72 of file Node.cpp.

References branchProperties_, branchProperties_, branchProperties_, branchProperties_, distanceToFather_, distanceToFather_, distanceToFather_, distanceToFather_, hasDistanceToFather(), hasName(), id_, id_, name_, name_, name_, name_, nodeProperties_, nodeProperties_, nodeProperties_, and nodeProperties_.

Referenced by bpp::NodeTemplate< NodeInfos >::operator=().

virtual bool bpp::Node::operator== ( const Node &  node ) const

inlinevirtual

Definition at line 687 of file Node.h.

References id_.

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

inline

Definition at line 497 of file Node.h.

References father_, and sons_.

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

inline

Definition at line 499 of file Node.h.

References father_, and sons_.

virtual void bpp::Node::removeBranchProperties ( )

inlinevirtual

Remove all branch properties.

Attached objects will not be deleted.

Definition at line 660 of file Node.h.

References branchProperties_.

virtual Clonable* bpp::Node::removeBranchProperty ( const std::string &  name ) throw (PropertyNotFoundException)

inlinevirtual

Definition at line 632 of file Node.h.

References branchProperties_, branchProperties_, and hasBranchProperty().

virtual Node* bpp::Node::removeFather ( )

inlinevirtual

Remove the father of this node.

Reimplemented in bpp::NodeTemplate< NodeInfos >.

Definition at line 368 of file Node.h.

References father_, and father_.

Referenced by removeSon().

virtual void bpp::Node::removeNodeProperties ( )

inlinevirtual

Remove all node properties.

Attached objects will not be deleted.

Definition at line 570 of file Node.h.

References nodeProperties_.

virtual Clonable* bpp::Node::removeNodeProperty ( const std::string &  name ) throw (PropertyNotFoundException)

inlinevirtual

Definition at line 542 of file Node.h.

References hasNodeProperty(), nodeProperties_, and nodeProperties_.

virtual Node* bpp::Node::removeSon ( size_t  pos ) throw (IndexOutOfBoundsException)

inlinevirtual

Definition at line 443 of file Node.h.

References removeFather(), sons_, sons_, sons_, and sons_.

Referenced by bpp::DRTreeParsimonyScore::doNNI(), bpp::DRTreeParsimonyScore::doNNI(), bpp::NNIHomogeneousTreeLikelihood::doNNI(), bpp::NNIHomogeneousTreeLikelihood::doNNI(), bpp::TreeTemplateTools::midRoot(), and removeSons().

virtual void bpp::Node::removeSon ( Node *  node ) throw (NodeNotFoundException, NullPointerException)

inlinevirtual

Definition at line 453 of file Node.h.

References sons_, sons_, and sons_.

virtual void bpp::Node::removeSons ( )

inlinevirtual

Definition at line 469 of file Node.h.

References removeSon(), and sons_.

virtual void bpp::Node::setBranchProperty ( const std::string &  name, const Clonable &  property  )

inlinevirtual

Set/add a branch property.

If no property with the same name is found, the new property will be added to the list. Conversely, the property will be deleted and replaced by the new one. If you want to keep a copy of the old property, consider using the removeBranchProperty function before.

Parameters

name	The name of the property to set.
property	The property object (will be cloned).

Definition at line 609 of file Node.h.

References branchProperties_, branchProperties_, and hasBranchProperty().

Referenced by bpp::Nhx::changeNamesToTags(), bpp::Nhx::changeTagsToNames(), bpp::TreeTemplateTools::midRoot(), bpp::TreeTemplateTools::parenthesisToNode(), bpp::TreeTemplateTools::parenthesisToNode(), and bpp::Nhx::setNodeProperties().

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

inlinevirtual

Set or update the distance toward the father node.

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

Parameters

distance

The new distance to the father node.

Definition at line 298 of file Node.h.

References distanceToFather_, distanceToFather_, and distanceToFather_.

Referenced by bpp::RHomogeneousClockTreeLikelihood::computeBranchLengthsFromHeights(), bpp::RHomogeneousClockTreeLikelihood::computeBranchLengthsFromHeights(), bpp::BioNJ::computeTree(), bpp::BioNJ::computeTree(), bpp::AbstractAgglomerativeDistanceMethod::computeTree(), bpp::AbstractAgglomerativeDistanceMethod::computeTree(), bpp::NNIHomogeneousTreeLikelihood::doNNI(), bpp::HierarchicalClustering::finalStep(), bpp::HierarchicalClustering::finalStep(), bpp::PGMA::finalStep(), bpp::PGMA::finalStep(), bpp::NeighborJoining::finalStep(), bpp::NeighborJoining::finalStep(), bpp::NeighborJoining::finalStep(), bpp::NeighborJoining::finalStep(), bpp::NeighborJoining::finalStep(), bpp::TreeTemplateTools::midRoot(), bpp::Nhx::parenthesisToNode(), bpp::TreeTemplateTools::parenthesisToNode(), bpp::TreeTemplateTools::setBranchLengths(), and bpp::TreeTemplateTools::setVoidBranchLengths().

virtual void bpp::Node::setFather ( Node *  node ) throw (NullPointerException)

inlinevirtual

Set the father node of this node.

Parameters

node	The father node.

Definition at line 354 of file Node.h.

References father_, and sons_.

virtual void bpp::Node::setId ( int  id )

inlinevirtual

Set this node's id.

Parameters

id	The new identity tag.

Definition at line 209 of file Node.h.

References id_.

Referenced by bpp::TreeTemplateTools::incrementAllIds(), bpp::TreeTemplateTools::midRoot(), bpp::TreeTemplateTools::parenthesisToNode(), bpp::TreeTemplateTools::parenthesisToNode(), and bpp::Nhx::setNodeProperties().

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

inlinevirtual

Give a name or update the name associated to the node.

Parameters

name	The name to give to the node.

Definition at line 246 of file Node.h.

References name_, name_, and name_.

Referenced by bpp::Nhx::parenthesisToNode(), bpp::TreeTemplateTools::parenthesisToNode(), and bpp::TreeTemplateTools::parenthesisToNode().

virtual void bpp::Node::setNodeProperty ( const std::string &  name, const Clonable &  property  )

inlinevirtual

Set/add a node property.

If no property with the same name is found, the new property will be added to the list. Conversely, the property will be deleted and replaced by the new one. If you want to keep a copy of the old property, consider using the removeNodeProperty function before.

Parameters

name	The name of the property to set.
property	The property object (will be cloned).

Definition at line 519 of file Node.h.

References hasNodeProperty(), nodeProperties_, and nodeProperties_.

Referenced by bpp::Nhx::changeNamesToTags(), bpp::Nhx::changeTagsToNames(), and bpp::Nhx::setNodeProperties().

virtual void bpp::Node::setSon ( size_t  pos, Node *  node  ) throw (IndexOutOfBoundsException, NullPointerException, NodePException)

inlinevirtual

Definition at line 429 of file Node.h.

References sons_, sons_, sons_, sons_, sons_, sons_, and sons_.

void Node::swap ( size_t  branch1, size_t  branch2  ) throw (IndexOutOfBoundsException)

virtual

Sons:

Definition at line 98 of file Node.cpp.

Referenced by bpp::TreeTemplateTools::orderTree_(), and bpp::TreeTemplateTools::orderTree_().

Member Data Documentation

std::map<std::string, Clonable*> bpp::Node::branchProperties_

mutableprotected

Definition at line 99 of file Node.h.

Referenced by deleteBranchProperties(), deleteBranchProperties(), deleteBranchProperties(), deleteBranchProperty(), deleteBranchProperty(), getBranchProperty(), getBranchProperty(), getBranchPropertyNames(), hasBranchProperty(), hasBranchProperty(), Node(), Node(), Node(), operator=(), operator=(), operator=(), operator=(), removeBranchProperties(), removeBranchProperty(), removeBranchProperty(), setBranchProperty(), setBranchProperty(), ~Node(), and ~Node().

double* bpp::Node::distanceToFather_

protected

Definition at line 97 of file Node.h.

Referenced by deleteDistanceToFather(), deleteDistanceToFather(), deleteDistanceToFather(), getDistanceToFather(), hasDistanceToFather(), Node(), Node(), operator=(), operator=(), operator=(), operator=(), setDistanceToFather(), setDistanceToFather(), setDistanceToFather(), ~Node(), and ~Node().

Node* bpp::Node::father_

protected

Definition at line 96 of file Node.h.

Referenced by bpp::NodeTemplate< NodeInfos >::getFather(), bpp::NodeTemplate< NodeInfos >::getFather(), getFather(), getFather(), getFatherId(), getNeighbors(), getNeighbors(), hasFather(), bpp::NodeTemplate< NodeInfos >::operator[](), bpp::NodeTemplate< NodeInfos >::operator[](), operator[](), operator[](), bpp::NodeTemplate< NodeInfos >::removeFather(), bpp::NodeTemplate< NodeInfos >::removeFather(), removeFather(), removeFather(), and setFather().

int bpp::Node::id_

protected

Definition at line 93 of file Node.h.

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

std::string* bpp::Node::name_

protected

Definition at line 94 of file Node.h.

Referenced by deleteName(), deleteName(), deleteName(), getName(), hasName(), Node(), Node(), operator=(), operator=(), operator=(), operator=(), setName(), setName(), setName(), ~Node(), and ~Node().

std::map<std::string, Clonable*> bpp::Node::nodeProperties_

mutableprotected

Definition at line 98 of file Node.h.

Referenced by deleteNodeProperties(), deleteNodeProperties(), deleteNodeProperties(), deleteNodeProperty(), deleteNodeProperty(), getNodeProperty(), getNodeProperty(), getNodePropertyNames(), hasNodeProperty(), hasNodeProperty(), Node(), Node(), Node(), operator=(), operator=(), operator=(), operator=(), removeNodeProperties(), removeNodeProperty(), removeNodeProperty(), setNodeProperty(), setNodeProperty(), ~Node(), and ~Node().

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

protected

Definition at line 95 of file Node.h.

Referenced by addSon(), addSon(), addSon(), addSon(), addSon(), addSon(), addSon(), addSon(), getNeighbors(), getNeighbors(), getNeighbors(), getNeighbors(), getNumberOfSons(), bpp::NodeTemplate< NodeInfos >::getSon(), bpp::NodeTemplate< NodeInfos >::getSon(), getSon(), getSon(), getSon(), getSon(), getSon(), getSon(), getSons(), getSonsId(), getSonsId(), getSonsId(), bpp::NodeTemplate< NodeInfos >::operator[](), bpp::NodeTemplate< NodeInfos >::operator[](), operator[](), operator[](), removeSon(), removeSon(), removeSon(), removeSon(), removeSon(), removeSon(), removeSon(), removeSons(), setFather(), setSon(), setSon(), setSon(), setSon(), setSon(), setSon(), and setSon().

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

• Bpp/Phyl/Node.h
• Bpp/Phyl/Node.cpp