bpp-phyl3  3.0.0
Public Member Functions | Protected Attributes | List of all members
bpp::Node Class Reference

The phylogenetic node class. More...

#include <Bpp/Phyl/Tree/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 ()
 
void addSubTree (const PhyloTree &tree, std::shared_ptr< PhyloNode > phyloNode)
 
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
 
virtual bool hasNoSon () 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
 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)
 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
 
virtual Node * getSon (size_t pos)
 
virtual void addSon (size_t pos, Node *node)
 
virtual void addSon (Node *node)
 
virtual void setSon (size_t pos, Node *node)
 
virtual Node * removeSon (size_t pos)
 
virtual void removeSon (Node *node)
 
virtual void removeSons ()
 
virtual void swap (size_t branch1, size_t branch2)
 
virtual size_t getSonPosition (const Node *son) const
 
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)
 
virtual const Clonable * getNodeProperty (const std::string &name) const
 
virtual Clonable * removeNodeProperty (const std::string &name)
 
virtual void deleteNodeProperty (const std::string &name)
 
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)
 
virtual const Clonable * getBranchProperty (const std::string &name) const
 
virtual Clonable * removeBranchProperty (const std::string &name)
 
virtual void deleteBranchProperty (const std::string &name)
 
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
 

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, optional 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 58 of file Node.h.

Constructor & Destructor Documentation

◆ Node() [1/5]

bpp::Node::Node ( )
inline

Build a new void Node object.

Definition at line 73 of file Node.h.

Referenced by addSubTree(), and clone().

◆ Node() [2/5]

bpp::Node::Node ( int  id)
inline

Build a new Node with specified id.

Definition at line 86 of file Node.h.

◆ Node() [3/5]

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

Build a new Node with specified name.

Definition at line 99 of file Node.h.

◆ Node() [4/5]

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

Build a new Node with specified id and name.

Definition at line 112 of file Node.h.

◆ Node() [5/5]

Node::Node ( const Node &  node)

Copy constructor.

Warning
This constructor copies all fields, excepted father and son node pointers.
Parameters
nodeThe node to copy.

Copy constructor:

Definition at line 22 of file Node.cpp.

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

◆ ~Node()

virtual bpp::Node::~Node ( )
inlinevirtual

Definition at line 144 of file Node.h.

References branchProperties_, distanceToFather_, name_, and nodeProperties_.

Member Function Documentation

◆ addSon() [1/2]

virtual void bpp::Node::addSon ( Node *  node)
inlinevirtual

Definition at line 386 of file Node.h.

References father_, and sons_.

◆ addSon() [2/2]

virtual void bpp::Node::addSon ( size_t  pos,
Node *  node 
)
inlinevirtual

Definition at line 374 of file Node.h.

References father_, and sons_.

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

◆ addSubTree()

void Node::addSubTree ( const PhyloTree &  tree,
std::shared_ptr< PhyloNode >  phyloNode 
)

Sons:

Definition at line 72 of file Node.cpp.

References addSon(), addSubTree(), bpp::AssociationTreeGraphImplObserver< class, class, class >::getIncomingEdges(), bpp::AssociationTreeGraphImplObserver< class, class, class >::getNodeIndex(), bpp::AssociationTreeGraphImplObserver< class, class, class >::getSons(), Node(), setBranchProperty(), setDistanceToFather(), setId(), setName(), and setNodeProperty().

Referenced by addSubTree(), and bpp::TreeTemplateTools::buildFromPhyloTree().

◆ clone()

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

Definition at line 141 of file Node.h.

References Node().

◆ degree()

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

Definition at line 463 of file Node.h.

References getNumberOfSons(), and hasFather().

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

◆ deleteBranchProperties()

virtual void bpp::Node::deleteBranchProperties ( )
inlinevirtual

Delete all branch properties.

Definition at line 644 of file Node.h.

References branchProperties_.

◆ deleteBranchProperty()

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

Definition at line 620 of file Node.h.

References branchProperties_, and hasBranchProperty().

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

◆ deleteDistanceToFather()

virtual void bpp::Node::deleteDistanceToFather ( )
inlinevirtual

Delete the distance to the father node.

Definition at line 276 of file Node.h.

References distanceToFather_.

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

◆ deleteName()

virtual void bpp::Node::deleteName ( )
inlinevirtual

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

Definition at line 223 of file Node.h.

References name_.

◆ deleteNodeProperties()

virtual void bpp::Node::deleteNodeProperties ( )
inlinevirtual

Delete all node properties.

Definition at line 554 of file Node.h.

References nodeProperties_.

◆ deleteNodeProperty()

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

Definition at line 530 of file Node.h.

References hasNodeProperty(), and nodeProperties_.

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

◆ getBootstrapValue()

double Node::getBootstrapValue ( ) const
virtual

Definition at line 168 of file Node.cpp.

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

◆ getBranchProperty() [1/2]

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

Definition at line 592 of file Node.h.

References branchProperties_, and hasBranchProperty().

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

◆ getBranchProperty() [2/2]

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

Definition at line 600 of file Node.h.

References branchProperties_, and hasBranchProperty().

◆ getBranchPropertyNames()

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

Definition at line 655 of file Node.h.

References branchProperties_, and bpp::MapTools::getKeys().

Referenced by bpp::PhyloTree::addSubTree(), bpp::TreeTemplateTools::getBranchPropertyNames(), and bpp::TreeTemplateTools::midRoot().

◆ getDistanceToFather()

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 250 of file Node.h.

References distanceToFather_, and hasDistanceToFather().

Referenced by bpp::PhyloTree::addSubTree(), bpp::BranchLengthsTreeDrawingListener::afterDrawBranch(), bpp::PhyloStatistics::computeForSubtree_(), bpp::LegacyRewardMappingTools::computeRewardVectors(), bpp::LegacySubstitutionMappingTools::computeSubstitutionVectors(), bpp::LegacySubstitutionMappingTools::computeSubstitutionVectorsMarginal(), bpp::LegacySubstitutionMappingTools::computeSubstitutionVectorsNoAveraging(), bpp::LegacySubstitutionMappingTools::computeSubstitutionVectorsNoAveragingMarginal(), bpp::AbstractHomogeneousTreeLikelihood::computeTransitionProbabilitiesForNode(), bpp::AbstractNonHomogeneousTreeLikelihood::computeTransitionProbabilitiesForNode(), bpp::RNonHomogeneousMixedTreeLikelihood::computeTransitionProbabilitiesForNode(), bpp::NonHomogeneousSequenceSimulator::dEvolveInternal(), bpp::TreeTemplateTools::dropSubtree(), bpp::NonHomogeneousSequenceSimulator::evolve(), bpp::PhylogramDrawBranchEvent::getBranchCursor(), bpp::TreeTemplateTools::getBranchLengths(), bpp::TreeTemplateTools::getHeight(), bpp::TreeTemplateTools::getHeights(), bpp::HierarchicalClustering::getParentNode(), bpp::PGMA::getParentNode(), bpp::TreeTemplateTools::getSubtreeMoments_(), bpp::TreeTemplateTools::getTotalLength(), bpp::NonHomogeneousSequenceSimulator::init(), bpp::TreeTemplateTools::midRoot(), bpp::Nhx::nodeToParenthesis(), bpp::TreeTemplateTools::nodeToParenthesis(), bpp::TreeTemplateTools::processDistsInSubtree_(), bpp::PhylogramPlot::recursivePlot_(), bpp::TreeTemplateTools::scaleTree(), bpp::Nhx::treeToParenthesis(), bpp::TreeTemplateTools::treeToParenthesis(), bpp::TreeTemplateTools::unresolveUncertainNodes(), bpp::LegacyRewardMappingTools::writeToStream(), and bpp::LegacySubstitutionMappingTools::writeToStream().

◆ getFather() [1/2]

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 313 of file Node.h.

References father_.

◆ getFather() [2/2]

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 306 of file Node.h.

References father_.

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

◆ getFatherId()

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

Definition at line 315 of file Node.h.

References father_, and getId().

◆ getId()

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

Get the node's id.

Returns
The identity tag of this node.

Definition at line 170 of file Node.h.

References id_.

Referenced by bpp::AbstractNonHomogeneousTreeLikelihood::AbstractNonHomogeneousTreeLikelihood(), bpp::PhyloTree::addSubTree(), bpp::BipartitionList::buildBitBipartitions(), bpp::PhyloTreeTools::buildFromTreeTemplate(), bpp::GlobalClockTreeLikelihoodFunctionWrapper::computeBranchLengthsFromHeights_(), bpp::RHomogeneousTreeLikelihood::computeDownSubtreeD2Likelihood(), bpp::RNonHomogeneousMixedTreeLikelihood::computeDownSubtreeD2Likelihood(), bpp::RNonHomogeneousTreeLikelihood::computeDownSubtreeD2Likelihood(), bpp::RHomogeneousTreeLikelihood::computeDownSubtreeDLikelihood(), bpp::RNonHomogeneousMixedTreeLikelihood::computeDownSubtreeDLikelihood(), bpp::RNonHomogeneousTreeLikelihood::computeDownSubtreeDLikelihood(), bpp::DRNonHomogeneousTreeLikelihood::computeLikelihoodAtNode_(), bpp::DRHomogeneousTreeLikelihood::computeLikelihoodAtNode_(), bpp::LegacyRewardMappingTools::computeRewardVectors(), bpp::DRHomogeneousTreeLikelihood::computeRootLikelihood(), bpp::DRNonHomogeneousTreeLikelihood::computeRootLikelihood(), bpp::DRTreeParsimonyScore::computeScoresForNode(), bpp::DRTreeParsimonyScore::computeScoresPostorder(), bpp::DRTreeParsimonyScore::computeScoresPostorderForNode(), bpp::DRTreeParsimonyScore::computeScoresPreorder(), bpp::DRTreeParsimonyScore::computeScoresPreorderForNode(), bpp::LegacySubstitutionMappingTools::computeSubstitutionVectors(), bpp::LegacySubstitutionMappingTools::computeSubstitutionVectorsMarginal(), bpp::LegacySubstitutionMappingTools::computeSubstitutionVectorsNoAveraging(), bpp::LegacySubstitutionMappingTools::computeSubstitutionVectorsNoAveragingMarginal(), bpp::RHomogeneousTreeLikelihood::computeSubtreeLikelihood(), bpp::RNonHomogeneousMixedTreeLikelihood::computeSubtreeLikelihood(), bpp::RNonHomogeneousTreeLikelihood::computeSubtreeLikelihood(), bpp::DRHomogeneousTreeLikelihood::computeSubtreeLikelihoodPostfix(), bpp::DRNonHomogeneousTreeLikelihood::computeSubtreeLikelihoodPostfix(), bpp::DRHomogeneousTreeLikelihood::computeSubtreeLikelihoodPrefix(), bpp::DRNonHomogeneousTreeLikelihood::computeSubtreeLikelihoodPrefix(), bpp::AbstractHomogeneousTreeLikelihood::computeTransitionProbabilitiesForNode(), bpp::AbstractNonHomogeneousTreeLikelihood::computeTransitionProbabilitiesForNode(), bpp::RNonHomogeneousMixedTreeLikelihood::computeTransitionProbabilitiesForNode(), bpp::RHomogeneousTreeLikelihood::computeTreeD2Likelihood(), bpp::RNonHomogeneousMixedTreeLikelihood::computeTreeD2Likelihood(), bpp::RNonHomogeneousTreeLikelihood::computeTreeD2Likelihood(), bpp::DRHomogeneousTreeLikelihood::computeTreeD2LikelihoodAtNode(), bpp::DRNonHomogeneousTreeLikelihood::computeTreeD2LikelihoodAtNode(), bpp::RHomogeneousTreeLikelihood::computeTreeDLikelihood(), bpp::RNonHomogeneousMixedTreeLikelihood::computeTreeDLikelihood(), bpp::RNonHomogeneousTreeLikelihood::computeTreeDLikelihood(), bpp::DRHomogeneousTreeLikelihood::computeTreeDLikelihoodAtNode(), bpp::DRNonHomogeneousTreeLikelihood::computeTreeDLikelihoodAtNode(), bpp::NonHomogeneousSequenceSimulator::dEvolveInternal(), bpp::DRHomogeneousTreeLikelihood::displayLikelihood(), bpp::DRNonHomogeneousTreeLikelihood::displayLikelihood(), bpp::RHomogeneousTreeLikelihood::displayLikelihood(), bpp::RNonHomogeneousTreeLikelihood::displayLikelihood(), bpp::NNIHomogeneousTreeLikelihood::doNNI(), bpp::InOrderTreeIterator::doStep(), bpp::TreeTemplateTools::getAncestorsId(), bpp::TreeTemplateTools::getBranchProperties(), getFatherId(), bpp::DRHomogeneousMixedTreeLikelihood::getFirstOrderDerivative(), bpp::DRNonHomogeneousTreeLikelihood::getFirstOrderDerivative(), bpp::DRHomogeneousTreeLikelihood::getFirstOrderDerivative(), bpp::TreeTemplateTools::getInnerNodesId(), bpp::TreeTemplateTools::getLeavesId(), bpp::PostOrderTreeIterator::getLeftMostPredecessor(), bpp::TreeTemplateTools::getNodeProperties(), bpp::TreeTemplateTools::getNodesId(), bpp::DRHomogeneousMixedTreeLikelihood::getSecondOrderDerivative(), bpp::DRNonHomogeneousTreeLikelihood::getSecondOrderDerivative(), bpp::DRHomogeneousTreeLikelihood::getSecondOrderDerivative(), getSonPosition(), bpp::TreeTemplateTools::incrementAllIds(), bpp::NonHomogeneousSequenceSimulator::init(), bpp::DRTreeParsimonyData::init_(), bpp::AbstractNonHomogeneousTreeLikelihood::init_(), bpp::DRASRTreeLikelihoodData::initLikelihoods(), bpp::DRASDRTreeLikelihoodData::initLikelihoods(), bpp::DRASRTreeLikelihoodData::initLikelihoodsWithPatterns(), bpp::TreeTemplateTools::nodeToParenthesis(), bpp::AbstractNonHomogeneousTreeLikelihood::operator=(), bpp::Nhx::propertiesToParenthesis(), bpp::LegacyMarginalAncestralStateReconstruction::recursiveMarginalAncestralStates(), bpp::DRASDRTreeLikelihoodData::reInit(), bpp::DRTreeParsimonyData::reInit_(), removeSon(), bpp::DRHomogeneousTreeLikelihood::resetLikelihoodArrays(), bpp::DRNonHomogeneousTreeLikelihood::resetLikelihoodArrays(), bpp::NNITopologySearch::searchBetter(), bpp::NNITopologySearch::searchFast(), bpp::TreeTemplateTools::searchFirstNodeWithId(), bpp::TreeTemplateTools::searchLeaf(), bpp::NNITopologySearch::searchPhyML(), bpp::AbstractHomogeneousTreeLikelihood::setModel(), bpp::AbstractNonHomogeneousTreeLikelihood::setSubstitutionModelSet(), bpp::NNIHomogeneousTreeLikelihood::testNNI(), bpp::DRTreeParsimonyScore::testNNI(), bpp::LegacyRewardMappingTools::writeToStream(), and bpp::LegacySubstitutionMappingTools::writeToStream().

◆ getName()

virtual std::string bpp::Node::getName ( ) const
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 203 of file Node.h.

References hasName(), and name_.

Referenced by bpp::PhyloTree::addSubTree(), bpp::LeafNamesTreeDrawingListener::afterDrawNode(), bpp::LabelInnerNodesTreeDrawingListener::afterDrawNode(), bpp::LabelCollapsedNodesTreeDrawingListener::afterDrawNode(), bpp::BipartitionList::buildBitBipartitions(), bpp::PhyloTreeTools::buildFromTreeTemplate(), bpp::RHomogeneousTreeLikelihood::displayLikelihood(), bpp::RNonHomogeneousTreeLikelihood::displayLikelihood(), bpp::TreeTemplateTools::getLeavesNames(), bpp::TreeTemplateTools::haveSameOrderedTopology(), bpp::DRTreeParsimonyData::init_(), bpp::DRASRTreeLikelihoodData::initLikelihoods(), bpp::DRASDRTreeLikelihoodData::initLikelihoods(), bpp::DRASRTreeLikelihoodData::initLikelihoodsWithPatterns(), bpp::Nhx::nodeToParenthesis(), bpp::TreeTemplateTools::nodeToParenthesis(), bpp::TreeTemplateTools::orderTree_(), bpp::TreeTemplateTools::processDistsInSubtree_(), bpp::LegacyMarginalAncestralStateReconstruction::recursiveMarginalAncestralStates(), bpp::TreeTemplateTools::searchLeaf(), bpp::Nhx::treeToParenthesis(), and bpp::TreeTemplateTools::treeToParenthesis().

◆ getNeighbors() [1/2]

vector< Node * > Node::getNeighbors ( )

Definition at line 139 of file Node.cpp.

References father_, hasFather(), and sons_.

◆ getNeighbors() [2/2]

vector< const Node * > Node::getNeighbors ( ) const

Definition at line 127 of file Node.cpp.

References father_, hasFather(), and sons_.

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

◆ getNodeProperty() [1/2]

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

Definition at line 502 of file Node.h.

References hasNodeProperty(), and nodeProperties_.

Referenced by bpp::PhyloTree::addSubTree(), bpp::PhyloTreeTools::buildFromTreeTemplate(), bpp::Nhx::changeNamesToTags(), bpp::Nhx::changeTagsToNames(), bpp::TreeTemplateTools::getNodeProperties(), and bpp::Nhx::propertiesToParenthesis().

◆ getNodeProperty() [2/2]

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

Definition at line 510 of file Node.h.

References hasNodeProperty(), and nodeProperties_.

◆ getNodePropertyNames()

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

Definition at line 565 of file Node.h.

References bpp::MapTools::getKeys(), and nodeProperties_.

Referenced by bpp::PhyloTree::addSubTree(), bpp::PhyloTreeTools::buildFromTreeTemplate(), and bpp::TreeTemplateTools::getNodePropertyNames().

◆ getNumberOfSons()

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

Definition at line 355 of file Node.h.

References sons_.

Referenced by bpp::PhyloTree::addSubTree(), bpp::BipartitionList::buildBitBipartitions(), bpp::Nhx::changeNamesToTags(), bpp::Nhx::changeTagsToNames(), bpp::TreeTemplateTools::cloneSubtree(), bpp::GlobalClockTreeLikelihoodFunctionWrapper::computeBranchLengthsFromHeights_(), bpp::RHomogeneousTreeLikelihood::computeDownSubtreeD2Likelihood(), bpp::RNonHomogeneousTreeLikelihood::computeDownSubtreeD2Likelihood(), bpp::RHomogeneousTreeLikelihood::computeDownSubtreeDLikelihood(), bpp::RNonHomogeneousTreeLikelihood::computeDownSubtreeDLikelihood(), bpp::PhyloStatistics::computeForSubtree_(), bpp::DRNonHomogeneousTreeLikelihood::computeLikelihoodAtNode_(), bpp::DRHomogeneousTreeLikelihood::computeLikelihoodAtNode_(), bpp::LegacyRewardMappingTools::computeRewardVectors(), bpp::DRHomogeneousTreeLikelihood::computeRootLikelihood(), bpp::DRNonHomogeneousTreeLikelihood::computeRootLikelihood(), bpp::DRTreeParsimonyScore::computeScoresPostorder(), bpp::DRTreeParsimonyScore::computeScoresPreorder(), bpp::LegacySubstitutionMappingTools::computeSubstitutionVectors(), bpp::LegacySubstitutionMappingTools::computeSubstitutionVectorsNoAveraging(), bpp::RHomogeneousTreeLikelihood::computeSubtreeLikelihood(), bpp::RNonHomogeneousTreeLikelihood::computeSubtreeLikelihood(), bpp::DRHomogeneousTreeLikelihood::computeSubtreeLikelihoodPostfix(), bpp::DRNonHomogeneousTreeLikelihood::computeSubtreeLikelihoodPostfix(), bpp::DRHomogeneousTreeLikelihood::computeSubtreeLikelihoodPrefix(), bpp::DRNonHomogeneousTreeLikelihood::computeSubtreeLikelihoodPrefix(), bpp::RHomogeneousTreeLikelihood::computeTreeD2Likelihood(), bpp::RNonHomogeneousTreeLikelihood::computeTreeD2Likelihood(), bpp::RHomogeneousTreeLikelihood::computeTreeDLikelihood(), bpp::RNonHomogeneousTreeLikelihood::computeTreeDLikelihood(), degree(), bpp::TreeTemplateTools::deleteBranchLengths(), bpp::TreeTemplateTools::deleteBranchProperties(), bpp::TreeTemplateTools::deleteNodeProperties(), bpp::NonHomogeneousSequenceSimulator::dEvolve(), bpp::NonHomogeneousSequenceSimulator::dEvolveInternal(), bpp::DRHomogeneousTreeLikelihood::displayLikelihood(), bpp::DRNonHomogeneousTreeLikelihood::displayLikelihood(), bpp::InOrderTreeIterator::doStep(), bpp::NonHomogeneousSequenceSimulator::evolveInternal(), bpp::TreeTemplateTools::getBranchLengths(), 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::PostOrderTreeIterator::getLeftMostPredecessor(), bpp::TreeTemplateTools::getNodeProperties(), bpp::TreeTemplateTools::getNodePropertyNames(), bpp::TreeTemplateTools::getNodesId(), bpp::TreeTemplateTools::getNumberOfBranches(), bpp::TreeTemplateTools::getNumberOfLeaves(), bpp::TreeTemplateTools::getNumberOfNodes(), bpp::DRNonHomogeneousTreeLikelihood::getSecondOrderDerivative(), bpp::TreeTemplateTools::getSubtreeMoments_(), bpp::TreeTemplateTools::getTotalLength(), hasNoSon(), bpp::TreeTemplateTools::haveSameOrderedTopology(), bpp::TreeTemplateTools::incrementAllIds(), bpp::DRTreeParsimonyData::init_(), bpp::DRASRTreeLikelihoodData::initLikelihoods(), bpp::DRASDRTreeLikelihoodData::initLikelihoods(), bpp::DRASRTreeLikelihoodData::initLikelihoodsWithPatterns(), bpp::TreeTemplateTools::isMultifurcating(), bpp::NonHomogeneousSequenceSimulator::multipleEvolve(), bpp::NonHomogeneousSequenceSimulator::multipleEvolveInternal(), bpp::PostOrderTreeIterator::next(), bpp::PreOrderTreeIterator::next(), bpp::Nhx::nodeToParenthesis(), bpp::TreeTemplateTools::nodeToParenthesis(), bpp::TreeTemplateTools::orderTree_(), bpp::TreeTemplateTools::processDistsInSubtree_(), bpp::LegacyMarginalAncestralStateReconstruction::recursiveMarginalAncestralStates(), bpp::CladogramPlot::recursivePlot_(), bpp::PhylogramPlot::recursivePlot_(), bpp::DRASDRTreeLikelihoodData::reInit(), bpp::DRTreeParsimonyData::reInit_(), bpp::DRHomogeneousTreeLikelihood::resetLikelihoodArrays(), bpp::DRNonHomogeneousTreeLikelihood::resetLikelihoodArrays(), bpp::TreeTemplateTools::scaleTree(), bpp::TreeTemplateTools::searchFirstNodeWithId(), bpp::TreeTemplateTools::searchLeaf(), bpp::TreeTemplateTools::setBranchLengths(), bpp::TreeTemplateTools::setVoidBranchLengths(), bpp::NonHomogeneousSequenceSimulator::simulateSite(), bpp::Nhx::treeToParenthesis(), bpp::TreeTemplateTools::treeToParenthesis(), and bpp::TreeTemplateTools::unresolveUncertainNodes().

◆ getSon() [1/2]

virtual Node* bpp::Node::getSon ( size_t  pos)
inlinevirtual

Reimplemented in bpp::NodeTemplate< NodeInfos >.

Definition at line 368 of file Node.h.

References sons_.

◆ getSon() [2/2]

virtual const Node* bpp::Node::getSon ( size_t  pos) const
inlinevirtual

Reimplemented in bpp::NodeTemplate< NodeInfos >.

Definition at line 362 of file Node.h.

References sons_.

Referenced by bpp::BipartitionList::buildBitBipartitions(), bpp::Nhx::changeNamesToTags(), bpp::Nhx::changeTagsToNames(), bpp::GlobalClockTreeLikelihoodFunctionWrapper::computeBranchLengthsFromHeights_(), bpp::RHomogeneousTreeLikelihood::computeDownSubtreeD2Likelihood(), bpp::RNonHomogeneousTreeLikelihood::computeDownSubtreeD2Likelihood(), bpp::RHomogeneousTreeLikelihood::computeDownSubtreeDLikelihood(), bpp::RNonHomogeneousTreeLikelihood::computeDownSubtreeDLikelihood(), bpp::DRNonHomogeneousTreeLikelihood::computeLikelihoodAtNode_(), bpp::DRHomogeneousTreeLikelihood::computeLikelihoodAtNode_(), bpp::LegacyRewardMappingTools::computeRewardVectors(), bpp::DRHomogeneousTreeLikelihood::computeRootLikelihood(), bpp::DRNonHomogeneousTreeLikelihood::computeRootLikelihood(), bpp::DRTreeParsimonyScore::computeScoresPostorder(), bpp::DRTreeParsimonyScore::computeScoresPreorder(), bpp::LegacySubstitutionMappingTools::computeSubstitutionVectors(), bpp::LegacySubstitutionMappingTools::computeSubstitutionVectorsNoAveraging(), bpp::RHomogeneousTreeLikelihood::computeSubtreeLikelihood(), bpp::RNonHomogeneousTreeLikelihood::computeSubtreeLikelihood(), bpp::DRHomogeneousTreeLikelihood::computeSubtreeLikelihoodPostfix(), bpp::DRNonHomogeneousTreeLikelihood::computeSubtreeLikelihoodPostfix(), bpp::DRHomogeneousTreeLikelihood::computeSubtreeLikelihoodPrefix(), bpp::DRNonHomogeneousTreeLikelihood::computeSubtreeLikelihoodPrefix(), bpp::RHomogeneousTreeLikelihood::computeTreeD2Likelihood(), bpp::RNonHomogeneousTreeLikelihood::computeTreeD2Likelihood(), bpp::RHomogeneousTreeLikelihood::computeTreeDLikelihood(), bpp::RNonHomogeneousTreeLikelihood::computeTreeDLikelihood(), bpp::TreeTemplateTools::deleteBranchLengths(), bpp::TreeTemplateTools::deleteBranchProperties(), bpp::TreeTemplateTools::deleteNodeProperties(), bpp::DRHomogeneousTreeLikelihood::displayLikelihood(), bpp::DRNonHomogeneousTreeLikelihood::displayLikelihood(), bpp::NNIHomogeneousTreeLikelihood::doNNI(), bpp::DRTreeParsimonyScore::doNNI(), bpp::InOrderTreeIterator::doStep(), bpp::TreeTemplateTools::getBranchLengths(), bpp::TreeTemplateTools::getBranchProperties(), bpp::TreeTemplateTools::getBranchPropertyNames(), bpp::TreeTemplateTools::getInnerNodesId(), bpp::TreeTemplateTools::getLeavesId(), bpp::TreeTemplateTools::getLeavesNames(), bpp::PostOrderTreeIterator::getLeftMostPredecessor(), bpp::TreeTemplateTools::getNodeProperties(), bpp::TreeTemplateTools::getNodePropertyNames(), bpp::TreeTemplateTools::getNodesId(), bpp::DRNonHomogeneousTreeLikelihood::getSecondOrderDerivative(), bpp::TreeTemplateTools::getSubtreeMoments_(), bpp::TreeTemplateTools::getTotalLength(), bpp::TreeTemplateTools::haveSameOrderedTopology(), bpp::TreeTemplateTools::incrementAllIds(), bpp::DRTreeParsimonyData::init_(), bpp::DRASDRTreeLikelihoodData::initLikelihoods(), bpp::TreeTemplateTools::isMultifurcating(), bpp::TreeTemplateTools::orderTree_(), bpp::TreeTemplateTools::processDistsInSubtree_(), bpp::LegacyMarginalAncestralStateReconstruction::recursiveMarginalAncestralStates(), bpp::DRASDRTreeLikelihoodData::reInit(), bpp::DRTreeParsimonyData::reInit_(), bpp::DRHomogeneousTreeLikelihood::resetLikelihoodArrays(), bpp::DRNonHomogeneousTreeLikelihood::resetLikelihoodArrays(), bpp::TreeTemplateTools::scaleTree(), bpp::TreeTemplateTools::searchFirstNodeWithId(), bpp::TreeTemplateTools::searchLeaf(), bpp::TreeTemplateTools::setBranchLengths(), bpp::TreeTemplateTools::setVoidBranchLengths(), swap(), bpp::NNIHomogeneousTreeLikelihood::testNNI(), bpp::DRTreeParsimonyScore::testNNI(), bpp::Nhx::treeToParenthesis(), bpp::TreeTemplateTools::treeToParenthesis(), and bpp::TreeTemplateTools::unresolveUncertainNodes().

◆ getSonPosition()

size_t Node::getSonPosition ( const Node *  son) const
virtual

Definition at line 151 of file Node.cpp.

References getId(), sons_, and bpp::TextTools::toString().

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

◆ getSons()

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

Definition at line 357 of file Node.h.

References sons_.

Referenced by bpp::TreeTemplateTools::getBestRootInSubtree_(), and bpp::TreeTemplateTools::midRoot().

◆ getSonsId()

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

Definition at line 179 of file Node.h.

References sons_.

◆ hasBootstrapValue()

bool Node::hasBootstrapValue ( ) const
virtual

Definition at line 163 of file Node.cpp.

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

◆ hasBranchProperty()

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

Definition at line 653 of file Node.h.

References branchProperties_.

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

◆ hasDistanceToFather()

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 288 of file Node.h.

References distanceToFather_.

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

◆ hasFather()

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

Tell if this node has a father node.

Definition at line 346 of file Node.h.

References father_.

Referenced by bpp::BipartitionList::buildBitBipartitions(), bpp::DRNonHomogeneousTreeLikelihood::computeLikelihoodAtNode_(), bpp::DRHomogeneousTreeLikelihood::computeLikelihoodAtNode_(), bpp::LegacyRewardMappingTools::computeRewardVectors(), bpp::DRTreeParsimonyScore::computeScoresPreorder(), bpp::LegacySubstitutionMappingTools::computeSubstitutionVectors(), bpp::LegacySubstitutionMappingTools::computeSubstitutionVectorsNoAveraging(), bpp::DRHomogeneousTreeLikelihood::computeSubtreeLikelihoodPrefix(), bpp::DRNonHomogeneousTreeLikelihood::computeSubtreeLikelihoodPrefix(), degree(), bpp::NonHomogeneousSequenceSimulator::dEvolveInternal(), bpp::DRHomogeneousTreeLikelihood::displayLikelihood(), bpp::DRNonHomogeneousTreeLikelihood::displayLikelihood(), bpp::NNIHomogeneousTreeLikelihood::doNNI(), bpp::DRTreeParsimonyScore::doNNI(), bpp::AbstractTreeDrawing::drawAtBranch(), bpp::TreeTemplateTools::dropSubtree(), bpp::NonHomogeneousSequenceSimulator::evolveInternal(), bpp::TreeTemplateTools::getAncestorsId(), getNeighbors(), bpp::TreeTemplateTools::getPathBetweenAnyTwoNodes(), bpp::DRTreeParsimonyData::init_(), bpp::DRASDRTreeLikelihoodData::initLikelihoods(), bpp::TreeTemplateTools::isRoot(), bpp::NonHomogeneousSequenceSimulator::multipleEvolveInternal(), bpp::TreeTemplateTools::orderTree_(), bpp::TreeTemplateTools::processDistsInSubtree_(), bpp::DRASDRTreeLikelihoodData::reInit(), bpp::DRTreeParsimonyData::reInit_(), bpp::DRHomogeneousTreeLikelihood::resetLikelihoodArrays(), bpp::DRNonHomogeneousTreeLikelihood::resetLikelihoodArrays(), bpp::TreeTemplateTools::scaleTree(), bpp::NNIHomogeneousTreeLikelihood::testNNI(), and bpp::DRTreeParsimonyScore::testNNI().

◆ hasName()

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

Tell is this node has a name.

Returns
True if name != 0.

Definition at line 234 of file Node.h.

References name_.

Referenced by bpp::PhyloTree::addSubTree(), bpp::LabelInnerNodesTreeDrawingListener::afterDrawNode(), bpp::LabelCollapsedNodesTreeDrawingListener::afterDrawNode(), bpp::PhyloTreeTools::buildFromTreeTemplate(), getName(), Node(), and operator=().

◆ hasNodeProperty()

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

Definition at line 563 of file Node.h.

References nodeProperties_.

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

◆ hasNoSon()

virtual bool bpp::Node::hasNoSon ( ) const
inlinevirtual

Definition at line 669 of file Node.h.

References getNumberOfSons().

Referenced by bpp::TreeTemplateTools::getLeavesNames(), bpp::TreeTemplateTools::haveSameOrderedTopology(), bpp::Nhx::nodeToParenthesis(), bpp::TreeTemplateTools::nodeToParenthesis(), bpp::TreeTemplateTools::orderTree_(), bpp::TreeTemplateTools::processDistsInSubtree_(), bpp::TreeTemplateTools::searchLeaf(), bpp::Nhx::treeToParenthesis(), and bpp::TreeTemplateTools::treeToParenthesis().

◆ isLeaf()

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

Definition at line 667 of file Node.h.

References degree().

Referenced by bpp::LeafNamesTreeDrawingListener::afterDrawNode(), bpp::GlobalClockTreeLikelihoodFunctionWrapper::computeBranchLengthsFromHeights_(), bpp::PhyloStatistics::computeForSubtree_(), bpp::DRNonHomogeneousTreeLikelihood::computeLikelihoodAtNode_(), bpp::DRHomogeneousTreeLikelihood::computeLikelihoodAtNode_(), bpp::DRHomogeneousTreeLikelihood::computeRootLikelihood(), bpp::DRNonHomogeneousTreeLikelihood::computeRootLikelihood(), bpp::DRTreeParsimonyScore::computeScoresPostorder(), bpp::DRTreeParsimonyScore::computeScoresPreorder(), bpp::RHomogeneousTreeLikelihood::computeSubtreeLikelihood(), bpp::RNonHomogeneousMixedTreeLikelihood::computeSubtreeLikelihood(), bpp::RNonHomogeneousTreeLikelihood::computeSubtreeLikelihood(), bpp::DRHomogeneousTreeLikelihood::computeSubtreeLikelihoodPostfix(), bpp::DRNonHomogeneousTreeLikelihood::computeSubtreeLikelihoodPostfix(), bpp::DRHomogeneousTreeLikelihood::computeSubtreeLikelihoodPrefix(), bpp::DRNonHomogeneousTreeLikelihood::computeSubtreeLikelihoodPrefix(), bpp::TreeTemplateTools::getInnerNodesId(), bpp::TreeTemplateTools::getLeavesId(), bpp::TreeTemplateTools::getNumberOfLeaves(), bpp::TreeTemplateTools::getSubtreeMoments_(), bpp::DRTreeParsimonyData::init_(), bpp::DRASRTreeLikelihoodData::initLikelihoods(), bpp::DRASDRTreeLikelihoodData::initLikelihoods(), bpp::DRASRTreeLikelihoodData::initLikelihoodsWithPatterns(), bpp::LegacyMarginalAncestralStateReconstruction::recursiveMarginalAncestralStates(), bpp::CladogramPlot::recursivePlot_(), bpp::PhylogramPlot::recursivePlot_(), bpp::DRASDRTreeLikelihoodData::reInit(), and bpp::DRTreeParsimonyData::reInit_().

◆ operator=()

Node & Node::operator= ( const Node &  node)

Assignation operator.

Warning
This operator copies all fields, excepted father and son node pointers.
Parameters
nodethe node to copy.
Returns
A reference toward this node.

Assignation operator:

Definition at line 42 of file Node.cpp.

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

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

◆ operator==()

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

Definition at line 663 of file Node.h.

References id_.

◆ operator[]() [1/2]

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

Definition at line 473 of file Node.h.

References father_, and sons_.

◆ operator[]() [2/2]

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

Definition at line 475 of file Node.h.

References father_, and sons_.

◆ removeBranchProperties()

virtual void bpp::Node::removeBranchProperties ( )
inlinevirtual

Remove all branch properties.

Attached objects will not be deleted.

Definition at line 636 of file Node.h.

References branchProperties_.

◆ removeBranchProperty()

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

Definition at line 608 of file Node.h.

References branchProperties_, and hasBranchProperty().

◆ removeFather()

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

Remove the father of this node.

Reimplemented in bpp::NodeTemplate< NodeInfos >.

Definition at line 336 of file Node.h.

References father_.

Referenced by removeSon().

◆ removeNodeProperties()

virtual void bpp::Node::removeNodeProperties ( )
inlinevirtual

Remove all node properties.

Attached objects will not be deleted.

Definition at line 546 of file Node.h.

References nodeProperties_.

◆ removeNodeProperty()

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

Definition at line 518 of file Node.h.

References hasNodeProperty(), and nodeProperties_.

◆ removeSon() [1/2]

virtual void bpp::Node::removeSon ( Node *  node)
inlinevirtual

Definition at line 421 of file Node.h.

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

◆ removeSon() [2/2]

virtual Node* bpp::Node::removeSon ( size_t  pos)
inlinevirtual

Definition at line 411 of file Node.h.

References removeFather(), and sons_.

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

◆ removeSons()

virtual void bpp::Node::removeSons ( )
inlinevirtual

Definition at line 437 of file Node.h.

References removeSon(), and sons_.

◆ setBranchProperty()

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

Definition at line 585 of file Node.h.

References branchProperties_, and hasBranchProperty().

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

◆ setDistanceToFather()

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
distanceThe new distance to the father node.

Definition at line 266 of file Node.h.

References distanceToFather_.

Referenced by addSubTree(), bpp::OptimizationTools::buildDistanceTree(), bpp::BioNJ::computeTree(), bpp::AbstractAgglomerativeDistanceMethod::computeTree(), bpp::NNIHomogeneousTreeLikelihood::doNNI(), bpp::HierarchicalClustering::finalStep(), bpp::NeighborJoining::finalStep(), bpp::PGMA::finalStep(), bpp::TreeTemplateTools::midRoot(), bpp::Nhx::parenthesisToNode(), bpp::TreeTemplateTools::parenthesisToNode(), bpp::TreeTemplateTools::scaleTree(), bpp::TreeTemplateTools::setBranchLengths(), bpp::TreeTemplateTools::setVoidBranchLengths(), and bpp::TreeTemplateTools::unresolveUncertainNodes().

◆ setFather()

virtual void bpp::Node::setFather ( Node *  node)
inlinevirtual

Set the father node of this node.

Parameters
nodeThe father node.

Definition at line 322 of file Node.h.

References father_, and sons_.

◆ setId()

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

Set this node's id.

Parameters
idThe new identity tag.

Definition at line 177 of file Node.h.

References id_.

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

◆ setName()

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

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

Parameters
nameThe name to give to the node.

Definition at line 214 of file Node.h.

References name_.

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

◆ setNodeProperty()

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

Definition at line 495 of file Node.h.

References hasNodeProperty(), and nodeProperties_.

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

◆ setSon()

virtual void bpp::Node::setSon ( size_t  pos,
Node *  node 
)
inlinevirtual

Definition at line 397 of file Node.h.

References father_, and sons_.

◆ swap()

void Node::swap ( size_t  branch1,
size_t  branch2 
)
virtual

Definition at line 111 of file Node.cpp.

References addSon(), getSon(), and removeSon().

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

Member Data Documentation

◆ branchProperties_

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

Definition at line 67 of file Node.h.

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

◆ distanceToFather_

double* bpp::Node::distanceToFather_
protected

Definition at line 65 of file Node.h.

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

◆ father_

Node* bpp::Node::father_
protected

Definition at line 64 of file Node.h.

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

◆ id_

int bpp::Node::id_
protected

Definition at line 61 of file Node.h.

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

◆ name_

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

Definition at line 62 of file Node.h.

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

◆ nodeProperties_

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

Definition at line 66 of file Node.h.

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

◆ sons_

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

Definition at line 63 of file Node.h.

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

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