bpp-phyl
2.2.0
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The NodeTemplate class. More...
#include <Bpp/Phyl/NodeTemplate.h>
Public Member Functions | |
NodeTemplate () | |
Build a new void NodeTemplate object. More... | |
NodeTemplate (int id) | |
Build a new NodeTemplate with specified id. More... | |
NodeTemplate (const std::string &name) | |
Build a new NodeTemplate with specified name. More... | |
NodeTemplate (int id, const std::string &name) | |
Build a new NodeTemplate with specified id and name. More... | |
virtual | ~NodeTemplate () |
const NodeTemplate< NodeInfos > * | getFather () const |
Get the father of this node is there is one. More... | |
NodeTemplate< NodeInfos > * | getFather () |
Get the father of this node is there is one. More... | |
NodeTemplate< NodeInfos > * | removeFather () |
Remove the father of this node. More... | |
const NodeTemplate< NodeInfos > * | getSon (size_t i) const throw (IndexOutOfBoundsException) |
NodeTemplate< NodeInfos > * | getSon (size_t i) throw (IndexOutOfBoundsException) |
std::vector< const NodeTemplate< NodeInfos > * > | getNeighbors () const |
std::vector< NodeTemplate< NodeInfos > * > | getNeighbors () |
NodeTemplate< NodeInfos > * | operator[] (int i) |
const NodeTemplate< NodeInfos > * | operator[] (int i) const |
virtual const NodeInfos & | getInfos () const |
virtual NodeInfos & | getInfos () |
virtual void | setInfos (const NodeInfos &infos) |
Set the information to be associated to this node. More... | |
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 int | getFatherId () const |
virtual void | setFather (Node *node) throw (NullPointerException) |
Set the father node 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 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) |
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 Member Functions | |
NodeTemplate (const Node &node) | |
Copy constructor. More... | |
NodeTemplate (const NodeTemplate< NodeInfos > &node) | |
Copy constructor. More... | |
NodeTemplate< NodeInfos > & | operator= (const NodeTemplate< NodeInfos > &node) |
Assignation operator. More... | |
NodeTemplate< NodeInfos > * | clone () 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_ |
Private Attributes | |
NodeInfos | infos_ |
Friends | |
class | TreeTemplateTools |
The NodeTemplate class.
This class inherits from the Node class. Its is a generic way to store any information to a node. A NodeTemplate only add the setInfos and getInfos methods, which set and retrieve a NodeInfo, whose type is given as a template of the class. This class is mainly for computation conveniency, one may define a NodeInfo class with several results attached. An example is provided in the PGMA class. Another way is to use a map<Node *, NodeInfos>, with the limitation of the map access. One may also wish to use the property system of the Node class, but properties are stored as in a map<string, Clonable *>, with the drawbacks of the slow map access and the systematic use of dynamic_cast<NodeInfo *> to convert from Clonable *.
This class redefines all constructors and access methods (get*) with return types as NodeTemplate and not Node (using covariant returns).
Definition at line 73 of file NodeTemplate.h.
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inline |
Build a new void NodeTemplate object.
Definition at line 87 of file NodeTemplate.h.
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inline |
Build a new NodeTemplate with specified id.
Definition at line 92 of file NodeTemplate.h.
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inline |
Build a new NodeTemplate with specified name.
Definition at line 97 of file NodeTemplate.h.
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inline |
Build a new NodeTemplate with specified id and name.
Definition at line 102 of file NodeTemplate.h.
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inlineprotected |
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inlineprotected |
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inlinevirtual |
Definition at line 137 of file NodeTemplate.h.
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inlinevirtualinherited |
Definition at line 407 of file Node.h.
References bpp::Node::sons_.
Referenced by bpp::DRTreeParsimonyScore::doNNI(), bpp::NNIHomogeneousTreeLikelihood::doNNI(), bpp::HierarchicalClustering::finalStep(), bpp::PGMA::finalStep(), bpp::NeighborJoining::finalStep(), bpp::HierarchicalClustering::getParentNode(), bpp::PGMA::getParentNode(), bpp::AbstractAgglomerativeDistanceMethod::getParentNode(), bpp::TreeTemplateTools::getRandomTree(), bpp::TreeTemplateTools::midRoot(), bpp::Nhx::parenthesisToNode(), bpp::TreeTemplateTools::parenthesisToNode(), bpp::BipartitionList::toTree(), and bpp::TreeTemplateTools::unresolveUncertainNodes().
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inlinevirtualinherited |
Definition at line 419 of file Node.h.
References bpp::Node::sons_.
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inlineprotected |
Definition at line 134 of file NodeTemplate.h.
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inlinevirtualinherited |
Definition at line 488 of file Node.h.
References bpp::Node::getNumberOfSons(), and bpp::Node::hasFather().
Referenced by bpp::DRTreeParsimonyScore::computeScoresForNode(), bpp::DRTreeParsimonyScore::computeScoresPostorderForNode(), bpp::DRTreeParsimonyScore::computeScoresPreorderForNode(), and bpp::Node::isLeaf().
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inlinevirtualinherited |
Delete all branch properties.
Definition at line 669 of file Node.h.
References bpp::Node::branchProperties_.
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inlinevirtualinherited |
Definition at line 645 of file Node.h.
References bpp::Node::branchProperties_, and bpp::Node::hasBranchProperty().
Referenced by bpp::Nhx::changeNamesToTags(), and bpp::Nhx::changeTagsToNames().
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inlinevirtualinherited |
Delete the distance to the father node.
Definition at line 309 of file Node.h.
References bpp::Node::distanceToFather_.
Referenced by bpp::TreeTemplateTools::deleteBranchLengths().
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inlinevirtualinherited |
Delete the name associated to this node (do nothing if there is no name).
Definition at line 256 of file Node.h.
References bpp::Node::name_.
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inlinevirtualinherited |
Delete all node properties.
Definition at line 579 of file Node.h.
References bpp::Node::nodeProperties_.
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inlinevirtualinherited |
Definition at line 555 of file Node.h.
References bpp::Node::hasNodeProperty(), and bpp::Node::nodeProperties_.
Referenced by bpp::Nhx::changeNamesToTags(), and bpp::Nhx::changeTagsToNames().
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virtualinherited |
Definition at line 146 of file Node.cpp.
References bpp::TreeTools::BOOTSTRAP, bpp::Node::getBranchProperty(), and bpp::Node::hasBranchProperty().
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inlinevirtualinherited |
Definition at line 617 of file Node.h.
References bpp::Node::branchProperties_, and bpp::Node::hasBranchProperty().
Referenced by bpp::BootstrapValuesTreeDrawingListener::afterDrawBranch(), bpp::Nhx::changeNamesToTags(), bpp::Nhx::changeTagsToNames(), bpp::Node::getBootstrapValue(), bpp::TreeTemplateTools::getBranchProperties(), bpp::TreeTemplateTools::midRoot(), bpp::TreeTemplateTools::nodeToParenthesis(), bpp::Nhx::propertiesToParenthesis(), bpp::TreeTemplateTools::treeToParenthesis(), and bpp::TreeTemplateTools::unresolveUncertainNodes().
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inlinevirtualinherited |
Definition at line 625 of file Node.h.
References bpp::Node::branchProperties_, and bpp::Node::hasBranchProperty().
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inlinevirtualinherited |
Definition at line 680 of file Node.h.
References bpp::Node::branchProperties_.
Referenced by bpp::TreeTemplateTools::getBranchPropertyNames(), and bpp::TreeTemplateTools::midRoot().
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inlinevirtualinherited |
Get the distance to the father node is there is one, otherwise throw a NodeException.
Definition at line 283 of file Node.h.
References bpp::Node::distanceToFather_, and bpp::Node::hasDistanceToFather().
Referenced by bpp::BranchLengthsTreeDrawingListener::afterDrawBranch(), bpp::PhyloStatistics::computeForSubtree_(), bpp::RewardMappingTools::computeRewardVectors(), bpp::SubstitutionMappingTools::computeSubstitutionVectors(), bpp::SubstitutionMappingTools::computeSubstitutionVectorsMarginal(), bpp::SubstitutionMappingTools::computeSubstitutionVectorsNoAveraging(), bpp::SubstitutionMappingTools::computeSubstitutionVectorsNoAveragingMarginal(), bpp::AbstractHomogeneousTreeLikelihood::computeTransitionProbabilitiesForNode(), bpp::RNonHomogeneousMixedTreeLikelihood::computeTransitionProbabilitiesForNode(), bpp::AbstractNonHomogeneousTreeLikelihood::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::TreeTemplateTools::midRoot(), bpp::Nhx::nodeToParenthesis(), bpp::TreeTemplateTools::nodeToParenthesis(), bpp::TreeTemplateTools::processDistsInSubtree_(), bpp::PhylogramPlot::recursivePlot_(), bpp::Nhx::treeToParenthesis(), bpp::TreeTemplateTools::treeToParenthesis(), and bpp::TreeTemplateTools::unresolveUncertainNodes().
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inlinevirtual |
Get the father of this node is there is one.
Reimplemented from bpp::Node.
Definition at line 141 of file NodeTemplate.h.
References bpp::Node::father_.
Referenced by bpp::NonHomogeneousSequenceSimulator::dEvolveInternal(), bpp::AbstractTreeDrawing::drawAtBranch(), bpp::NonHomogeneousSequenceSimulator::evolveInternal(), and bpp::NonHomogeneousSequenceSimulator::multipleEvolveInternal().
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inlinevirtual |
Get the father of this node is there is one.
Reimplemented from bpp::Node.
Definition at line 143 of file NodeTemplate.h.
References bpp::Node::father_.
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inlinevirtualinherited |
Definition at line 348 of file Node.h.
References bpp::Node::father_, and bpp::Node::getId().
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inlinevirtualinherited |
Get the node's id.
Definition at line 203 of file Node.h.
References bpp::Node::id_.
Referenced by bpp::AbstractNonHomogeneousTreeLikelihood::AbstractNonHomogeneousTreeLikelihood(), bpp::BipartitionList::buildBitBipartitions(), bpp::RHomogeneousClockTreeLikelihood::computeBranchLengthsFromHeights(), bpp::GlobalClockTreeLikelihoodFunctionWrapper::computeBranchLengthsFromHeights_(), 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::RewardMappingTools::computeRewardVectors(), bpp::DRHomogeneousTreeLikelihood::computeRootLikelihood(), bpp::DRNonHomogeneousTreeLikelihood::computeRootLikelihood(), bpp::DRTreeParsimonyScore::computeScoresForNode(), bpp::DRTreeParsimonyScore::computeScoresPostorder(), bpp::DRTreeParsimonyScore::computeScoresPostorderForNode(), bpp::DRTreeParsimonyScore::computeScoresPreorder(), bpp::DRTreeParsimonyScore::computeScoresPreorderForNode(), bpp::SubstitutionMappingTools::computeSubstitutionVectors(), bpp::SubstitutionMappingTools::computeSubstitutionVectorsMarginal(), bpp::SubstitutionMappingTools::computeSubstitutionVectorsNoAveraging(), bpp::SubstitutionMappingTools::computeSubstitutionVectorsNoAveragingMarginal(), bpp::RHomogeneousTreeLikelihood::computeSubtreeLikelihood(), bpp::RNonHomogeneousTreeLikelihood::computeSubtreeLikelihood(), bpp::RNonHomogeneousMixedTreeLikelihood::computeSubtreeLikelihood(), bpp::DRHomogeneousTreeLikelihood::computeSubtreeLikelihoodPostfix(), bpp::DRNonHomogeneousTreeLikelihood::computeSubtreeLikelihoodPostfix(), bpp::DRHomogeneousTreeLikelihood::computeSubtreeLikelihoodPrefix(), bpp::DRNonHomogeneousTreeLikelihood::computeSubtreeLikelihoodPrefix(), bpp::AbstractHomogeneousTreeLikelihood::computeTransitionProbabilitiesForNode(), bpp::RNonHomogeneousMixedTreeLikelihood::computeTransitionProbabilitiesForNode(), bpp::AbstractNonHomogeneousTreeLikelihood::computeTransitionProbabilitiesForNode(), bpp::RHomogeneousTreeLikelihood::computeTreeD2Likelihood(), bpp::RNonHomogeneousTreeLikelihood::computeTreeD2Likelihood(), bpp::RNonHomogeneousMixedTreeLikelihood::computeTreeD2Likelihood(), bpp::DRHomogeneousTreeLikelihood::computeTreeD2LikelihoodAtNode(), bpp::DRNonHomogeneousTreeLikelihood::computeTreeD2LikelihoodAtNode(), bpp::RHomogeneousTreeLikelihood::computeTreeDLikelihood(), bpp::RNonHomogeneousTreeLikelihood::computeTreeDLikelihood(), bpp::RNonHomogeneousMixedTreeLikelihood::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::TreeTemplateTools::getAncestorsId(), bpp::TreeTemplateTools::getBranchProperties(), bpp::Node::getFatherId(), bpp::TreeTemplateTools::getInnerNodesId(), bpp::TreeTemplateTools::getLeavesId(), bpp::AbstractTreeDrawing::getNodeAt(), bpp::AbstractTreeDrawing::getNodePosition(), bpp::TreeTemplateTools::getNodeProperties(), bpp::TreeTemplateTools::getNodesId(), bpp::DRNonHomogeneousTreeLikelihood::getSecondOrderDerivative(), 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::MarginalAncestralStateReconstruction::recursiveMarginalAncestralStates(), bpp::DRTreeParsimonyData::reInit(), bpp::DRASDRTreeLikelihoodData::reInit(), bpp::DRHomogeneousTreeLikelihood::resetLikelihoodArrays(), bpp::DRNonHomogeneousTreeLikelihood::resetLikelihoodArrays(), bpp::NNITopologySearch::searchBetter(), bpp::NNITopologySearch::searchFast(), bpp::TreeTemplateTools::searchFirstNodeWithId(), bpp::NNITopologySearch::searchPhyML(), bpp::AbstractHomogeneousTreeLikelihood::setSubstitutionModel(), bpp::AbstractNonHomogeneousTreeLikelihood::setSubstitutionModelSet(), bpp::DRTreeParsimonyScore::testNNI(), and bpp::NNIHomogeneousTreeLikelihood::testNNI().
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inlinevirtual |
Definition at line 179 of file NodeTemplate.h.
References bpp::NodeTemplate< NodeInfos >::infos_.
Referenced by bpp::LabelInnerNodesTreeDrawingListener::afterDrawNode(), bpp::LabelCollapsedNodesTreeDrawingListener::afterDrawNode(), bpp::NonHomogeneousSequenceSimulator::dEvolve(), bpp::NonHomogeneousSequenceSimulator::dEvolveInternal(), bpp::AbstractTreeDrawing::drawAtBranch(), bpp::AbstractTreeDrawing::drawAtNode(), bpp::NonHomogeneousSequenceSimulator::evolve(), bpp::NonHomogeneousSequenceSimulator::evolveInternal(), bpp::AbstractTreeDrawing::getNodeAt(), bpp::AbstractTreeDrawing::getNodePosition(), bpp::NonHomogeneousSequenceSimulator::init(), bpp::NonHomogeneousSequenceSimulator::multipleEvolve(), bpp::NonHomogeneousSequenceSimulator::multipleEvolveInternal(), bpp::PhylogramPlot::recursivePlot_(), bpp::CladogramPlot::recursivePlot_(), and bpp::NonHomogeneousSequenceSimulator::simulateSite().
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inlinevirtual |
Definition at line 184 of file NodeTemplate.h.
References bpp::NodeTemplate< NodeInfos >::infos_.
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inlinevirtualinherited |
Get the name associated to this node, if there is one, otherwise throw a NodeException.
Definition at line 236 of file Node.h.
References bpp::Node::hasName(), and bpp::Node::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::Nhx::nodeToParenthesis(), bpp::TreeTemplateTools::nodeToParenthesis(), bpp::TreeTemplateTools::orderTree_(), bpp::TreeTemplateTools::processDistsInSubtree_(), bpp::MarginalAncestralStateReconstruction::recursiveMarginalAncestralStates(), bpp::Nhx::treeToParenthesis(), and bpp::TreeTemplateTools::treeToParenthesis().
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Definition at line 151 of file NodeTemplate.h.
References bpp::Node::getNeighbors().
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Definition at line 160 of file NodeTemplate.h.
References bpp::Node::getNeighbors().
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inlinevirtualinherited |
Definition at line 527 of file Node.h.
References bpp::Node::hasNodeProperty(), and bpp::Node::nodeProperties_.
Referenced by bpp::Nhx::changeNamesToTags(), bpp::Nhx::changeTagsToNames(), bpp::TreeTemplateTools::getNodeProperties(), and bpp::Nhx::propertiesToParenthesis().
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inlinevirtualinherited |
Definition at line 535 of file Node.h.
References bpp::Node::hasNodeProperty(), and bpp::Node::nodeProperties_.
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inlinevirtualinherited |
Definition at line 590 of file Node.h.
References bpp::Node::nodeProperties_.
Referenced by bpp::TreeTemplateTools::getNodePropertyNames().
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inlinevirtualinherited |
Definition at line 388 of file Node.h.
References bpp::Node::sons_.
Referenced by 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::DRHomogeneousTreeLikelihood::computeLikelihoodAtNode_(), bpp::DRNonHomogeneousTreeLikelihood::computeLikelihoodAtNode_(), bpp::RewardMappingTools::computeRewardVectors(), 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::DRNonHomogeneousTreeLikelihood::computeSubtreeLikelihoodPostfix(), bpp::DRHomogeneousTreeLikelihood::computeSubtreeLikelihoodPrefix(), bpp::DRNonHomogeneousTreeLikelihood::computeSubtreeLikelihoodPrefix(), bpp::RHomogeneousTreeLikelihood::computeTreeD2Likelihood(), bpp::RNonHomogeneousTreeLikelihood::computeTreeD2Likelihood(), bpp::RHomogeneousTreeLikelihood::computeTreeDLikelihood(), bpp::RNonHomogeneousTreeLikelihood::computeTreeDLikelihood(), bpp::Node::degree(), bpp::TreeTemplateTools::deleteBranchLengths(), bpp::NonHomogeneousSequenceSimulator::dEvolve(), bpp::NonHomogeneousSequenceSimulator::dEvolveInternal(), bpp::DRHomogeneousTreeLikelihood::displayLikelihood(), bpp::DRNonHomogeneousTreeLikelihood::displayLikelihood(), bpp::NonHomogeneousSequenceSimulator::evolveInternal(), bpp::TreeTemplateTools::getBranchesId(), 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::getNodePropertyNames(), bpp::TreeTemplateTools::getNodesId(), bpp::TreeTemplateTools::getNumberOfLeaves(), bpp::TreeTemplateTools::getNumberOfNodes(), bpp::DRNonHomogeneousTreeLikelihood::getSecondOrderDerivative(), bpp::TreeTemplateTools::getSubtreeMoments_(), bpp::TreeTemplateTools::haveSameOrderedTopology(), bpp::TreeTemplateTools::incrementAllIds(), bpp::TreeTemplateTools::isMultifurcating(), bpp::NonHomogeneousSequenceSimulator::multipleEvolve(), bpp::NonHomogeneousSequenceSimulator::multipleEvolveInternal(), bpp::Nhx::nodeToParenthesis(), bpp::TreeTemplateTools::nodeToParenthesis(), bpp::TreeTemplateTools::orderTree_(), bpp::TreeTemplateTools::processDistsInSubtree_(), bpp::MarginalAncestralStateReconstruction::recursiveMarginalAncestralStates(), bpp::PhylogramPlot::recursivePlot_(), bpp::CladogramPlot::recursivePlot_(), bpp::DRHomogeneousTreeLikelihood::resetLikelihoodArrays(), bpp::DRNonHomogeneousTreeLikelihood::resetLikelihoodArrays(), bpp::TreeTemplateTools::searchFirstNodeWithId(), bpp::TreeTemplateTools::setBranchLengths(), bpp::TreeTemplateTools::setVoidBranchLengths(), bpp::NonHomogeneousSequenceSimulator::simulateSite(), bpp::Nhx::treeToParenthesis(), bpp::TreeTemplateTools::treeToParenthesis(), and bpp::TreeTemplateTools::unresolveUncertainNodes().
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inlinevirtual |
Reimplemented from bpp::Node.
Definition at line 147 of file NodeTemplate.h.
References bpp::Node::sons_.
Referenced by bpp::NonHomogeneousSequenceSimulator::dEvolve(), bpp::NonHomogeneousSequenceSimulator::dEvolveInternal(), bpp::NonHomogeneousSequenceSimulator::evolveInternal(), bpp::NonHomogeneousSequenceSimulator::multipleEvolve(), bpp::NonHomogeneousSequenceSimulator::multipleEvolveInternal(), bpp::PhylogramPlot::recursivePlot_(), bpp::CladogramPlot::recursivePlot_(), and bpp::NonHomogeneousSequenceSimulator::simulateSite().
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inlinevirtual |
Reimplemented from bpp::Node.
Definition at line 149 of file NodeTemplate.h.
References bpp::Node::sons_.
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virtualinherited |
Definition at line 130 of file Node.cpp.
Referenced by bpp::DRTreeParsimonyScore::doNNI(), bpp::NNIHomogeneousTreeLikelihood::doNNI(), bpp::DRTreeParsimonyScore::testNNI(), and bpp::NNIHomogeneousTreeLikelihood::testNNI().
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inlinevirtualinherited |
Definition at line 390 of file Node.h.
References bpp::Node::sons_.
Referenced by bpp::TreeTemplateTools::getBestRootInSubtree_(), and bpp::TreeTemplateTools::midRoot().
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inlinevirtualinherited |
Definition at line 212 of file Node.h.
References bpp::Node::sons_.
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virtualinherited |
Definition at line 141 of file Node.cpp.
References bpp::TreeTools::BOOTSTRAP, and bpp::Node::hasBranchProperty().
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inlinevirtualinherited |
Definition at line 678 of file Node.h.
References bpp::Node::branchProperties_.
Referenced by bpp::BootstrapValuesTreeDrawingListener::afterDrawBranch(), bpp::Nhx::changeNamesToTags(), bpp::Nhx::changeTagsToNames(), bpp::Node::deleteBranchProperty(), bpp::Node::getBootstrapValue(), bpp::TreeTemplateTools::getBranchProperties(), bpp::Node::getBranchProperty(), bpp::Node::hasBootstrapValue(), bpp::TreeTemplateTools::nodeToParenthesis(), bpp::Nhx::propertiesToParenthesis(), bpp::Node::removeBranchProperty(), bpp::Node::setBranchProperty(), bpp::TreeTemplateTools::treeToParenthesis(), and bpp::TreeTemplateTools::unresolveUncertainNodes().
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inlinevirtualinherited |
Tell is this node has a distance to the father.
Definition at line 321 of file Node.h.
References bpp::Node::distanceToFather_.
Referenced by bpp::BranchLengthsTreeDrawingListener::afterDrawBranch(), bpp::PhyloStatistics::computeForSubtree_(), bpp::Node::getDistanceToFather(), bpp::Node::Node(), bpp::Nhx::nodeToParenthesis(), bpp::TreeTemplateTools::nodeToParenthesis(), bpp::Node::operator=(), bpp::PhylogramPlot::recursivePlot_(), bpp::TreeTemplateTools::setVoidBranchLengths(), bpp::Nhx::treeToParenthesis(), and bpp::TreeTemplateTools::treeToParenthesis().
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inlinevirtualinherited |
Tell if this node has a father node.
Definition at line 379 of file Node.h.
References bpp::Node::father_.
Referenced by bpp::BipartitionList::buildBitBipartitions(), bpp::DRHomogeneousTreeLikelihood::computeLikelihoodAtNode_(), bpp::DRNonHomogeneousTreeLikelihood::computeLikelihoodAtNode_(), bpp::RewardMappingTools::computeRewardVectors(), bpp::DRTreeParsimonyScore::computeScoresPreorder(), bpp::SubstitutionMappingTools::computeSubstitutionVectors(), bpp::SubstitutionMappingTools::computeSubstitutionVectorsNoAveraging(), bpp::DRHomogeneousTreeLikelihood::computeSubtreeLikelihoodPrefix(), bpp::DRNonHomogeneousTreeLikelihood::computeSubtreeLikelihoodPrefix(), bpp::Node::degree(), bpp::NonHomogeneousSequenceSimulator::dEvolveInternal(), bpp::DRHomogeneousTreeLikelihood::displayLikelihood(), bpp::DRNonHomogeneousTreeLikelihood::displayLikelihood(), bpp::DRTreeParsimonyScore::doNNI(), bpp::NNIHomogeneousTreeLikelihood::doNNI(), bpp::AbstractTreeDrawing::drawAtBranch(), bpp::NonHomogeneousSequenceSimulator::evolveInternal(), bpp::TreeTemplateTools::getAncestorsId(), bpp::Node::getNeighbors(), bpp::TreeTemplateTools::getPathBetweenAnyTwoNodes(), bpp::TreeTemplateTools::isRoot(), bpp::NonHomogeneousSequenceSimulator::multipleEvolveInternal(), bpp::TreeTemplateTools::orderTree_(), bpp::TreeTemplateTools::processDistsInSubtree_(), bpp::DRHomogeneousTreeLikelihood::resetLikelihoodArrays(), bpp::DRNonHomogeneousTreeLikelihood::resetLikelihoodArrays(), bpp::DRTreeParsimonyScore::testNNI(), and bpp::NNIHomogeneousTreeLikelihood::testNNI().
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inlinevirtualinherited |
Tell is this node has a name.
Definition at line 267 of file Node.h.
References bpp::Node::name_.
Referenced by bpp::LabelInnerNodesTreeDrawingListener::afterDrawNode(), bpp::LabelCollapsedNodesTreeDrawingListener::afterDrawNode(), bpp::Node::getName(), bpp::Node::Node(), bpp::Node::operator=(), and bpp::TreeTemplateTools::treeToParenthesis().
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inlinevirtualinherited |
Definition at line 588 of file Node.h.
References bpp::Node::nodeProperties_.
Referenced by bpp::Nhx::changeNamesToTags(), bpp::Nhx::changeTagsToNames(), bpp::Node::deleteNodeProperty(), bpp::TreeTemplateTools::getNodeProperties(), bpp::Node::getNodeProperty(), bpp::Nhx::propertiesToParenthesis(), bpp::Node::removeNodeProperty(), and bpp::Node::setNodeProperty().
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inlinevirtualinherited |
Definition at line 692 of file Node.h.
References bpp::Node::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::computeScoresPreorder(), bpp::RHomogeneousTreeLikelihood::computeSubtreeLikelihood(), bpp::RNonHomogeneousTreeLikelihood::computeSubtreeLikelihood(), bpp::RNonHomogeneousMixedTreeLikelihood::computeSubtreeLikelihood(), bpp::DRHomogeneousTreeLikelihood::computeSubtreeLikelihoodPostfix(), bpp::DRNonHomogeneousTreeLikelihood::computeSubtreeLikelihoodPostfix(), bpp::DRHomogeneousTreeLikelihood::computeSubtreeLikelihoodPrefix(), bpp::DRNonHomogeneousTreeLikelihood::computeSubtreeLikelihoodPrefix(), bpp::TreeTemplateTools::getInnerNodesId(), bpp::TreeTemplateTools::getLeavesId(), bpp::TreeTemplateTools::getLeavesNames(), bpp::TreeTemplateTools::getNumberOfLeaves(), bpp::TreeTemplateTools::getSubtreeMoments_(), bpp::TreeTemplateTools::haveSameOrderedTopology(), bpp::DRASDRTreeLikelihoodData::initLikelihoods(), bpp::Nhx::nodeToParenthesis(), bpp::TreeTemplateTools::nodeToParenthesis(), bpp::TreeTemplateTools::orderTree_(), bpp::TreeTemplateTools::processDistsInSubtree_(), bpp::MarginalAncestralStateReconstruction::recursiveMarginalAncestralStates(), bpp::PhylogramPlot::recursivePlot_(), bpp::CladogramPlot::recursivePlot_(), bpp::Nhx::treeToParenthesis(), and bpp::TreeTemplateTools::treeToParenthesis().
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inlineprotected |
Assignation operator.
node | the node to copy. |
Definition at line 127 of file NodeTemplate.h.
References bpp::NodeTemplate< NodeInfos >::infos_, and bpp::Node::operator=().
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inlinevirtualinherited |
Definition at line 688 of file Node.h.
References bpp::Node::id_.
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inline |
Definition at line 169 of file NodeTemplate.h.
References bpp::Node::father_, and bpp::Node::sons_.
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inline |
Definition at line 171 of file NodeTemplate.h.
References bpp::Node::father_, and bpp::Node::sons_.
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inlinevirtualinherited |
Remove all branch properties.
Attached objects will not be deleted.
Definition at line 661 of file Node.h.
References bpp::Node::branchProperties_.
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inlinevirtualinherited |
Definition at line 633 of file Node.h.
References bpp::Node::branchProperties_, and bpp::Node::hasBranchProperty().
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inlinevirtual |
Remove the father of this node.
Reimplemented from bpp::Node.
Definition at line 145 of file NodeTemplate.h.
References bpp::Node::father_.
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inlinevirtualinherited |
Remove all node properties.
Attached objects will not be deleted.
Definition at line 571 of file Node.h.
References bpp::Node::nodeProperties_.
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inlinevirtualinherited |
Definition at line 543 of file Node.h.
References bpp::Node::hasNodeProperty(), and bpp::Node::nodeProperties_.
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inlinevirtualinherited |
Definition at line 444 of file Node.h.
References bpp::Node::removeFather(), and bpp::Node::sons_.
Referenced by bpp::DRTreeParsimonyScore::doNNI(), bpp::NNIHomogeneousTreeLikelihood::doNNI(), bpp::TreeTemplateTools::midRoot(), bpp::Node::removeSons(), and bpp::TreeTemplateTools::unresolveUncertainNodes().
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inlinevirtualinherited |
Definition at line 454 of file Node.h.
References bpp::Node::sons_.
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inlinevirtualinherited |
Definition at line 470 of file Node.h.
References bpp::Node::removeSon(), and bpp::Node::sons_.
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inlinevirtualinherited |
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.
name | The name of the property to set. |
property | The property object (will be cloned). |
Definition at line 610 of file Node.h.
References bpp::Node::branchProperties_, and bpp::Node::hasBranchProperty().
Referenced by bpp::Nhx::changeNamesToTags(), bpp::Nhx::changeTagsToNames(), bpp::TreeTemplateTools::midRoot(), bpp::TreeTemplateTools::parenthesisToNode(), and bpp::Nhx::setNodeProperties().
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inlinevirtualinherited |
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.
distance | The new distance to the father node. |
Definition at line 299 of file Node.h.
References bpp::Node::distanceToFather_.
Referenced by bpp::RHomogeneousClockTreeLikelihood::computeBranchLengthsFromHeights(), bpp::BioNJ::computeTree(), bpp::AbstractAgglomerativeDistanceMethod::computeTree(), bpp::NNIHomogeneousTreeLikelihood::doNNI(), bpp::HierarchicalClustering::finalStep(), bpp::PGMA::finalStep(), bpp::NeighborJoining::finalStep(), bpp::TreeTemplateTools::midRoot(), bpp::Nhx::parenthesisToNode(), bpp::TreeTemplateTools::parenthesisToNode(), bpp::TreeTemplateTools::setBranchLengths(), bpp::TreeTemplateTools::setVoidBranchLengths(), and bpp::TreeTemplateTools::unresolveUncertainNodes().
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inlinevirtualinherited |
Set the father node of this node.
node | The father node. |
Definition at line 355 of file Node.h.
References bpp::Node::father_, and bpp::Node::sons_.
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inlinevirtualinherited |
Set this node's id.
id | The new identity tag. |
Definition at line 210 of file Node.h.
References bpp::Node::id_.
Referenced by bpp::TreeTemplateTools::incrementAllIds(), bpp::TreeTemplateTools::midRoot(), bpp::TreeTemplateTools::parenthesisToNode(), and bpp::Nhx::setNodeProperties().
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inlinevirtual |
Set the information to be associated to this node.
infos | An information object. |
Definition at line 191 of file NodeTemplate.h.
References bpp::NodeTemplate< NodeInfos >::infos_.
Referenced by bpp::HierarchicalClustering::getLeafNode(), and bpp::PGMA::getLeafNode().
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inlinevirtualinherited |
Give a name or update the name associated to the node.
name | The name to give to the node. |
Definition at line 247 of file Node.h.
References bpp::Node::name_.
Referenced by bpp::Nhx::parenthesisToNode(), and bpp::TreeTemplateTools::parenthesisToNode().
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inlinevirtualinherited |
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.
name | The name of the property to set. |
property | The property object (will be cloned). |
Definition at line 520 of file Node.h.
References bpp::Node::hasNodeProperty(), and bpp::Node::nodeProperties_.
Referenced by bpp::Nhx::changeNamesToTags(), bpp::Nhx::changeTagsToNames(), and bpp::Nhx::setNodeProperties().
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inlinevirtualinherited |
Definition at line 430 of file Node.h.
References bpp::Node::sons_.
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virtualinherited |
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friend |
Definition at line 76 of file NodeTemplate.h.
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mutableprotectedinherited |
Definition at line 100 of file Node.h.
Referenced by bpp::Node::deleteBranchProperties(), bpp::Node::deleteBranchProperty(), bpp::Node::getBranchProperty(), bpp::Node::getBranchPropertyNames(), bpp::Node::hasBranchProperty(), bpp::Node::Node(), bpp::Node::operator=(), bpp::Node::removeBranchProperties(), bpp::Node::removeBranchProperty(), bpp::Node::setBranchProperty(), and bpp::Node::~Node().
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protectedinherited |
Definition at line 98 of file Node.h.
Referenced by bpp::Node::deleteDistanceToFather(), bpp::Node::getDistanceToFather(), bpp::Node::hasDistanceToFather(), bpp::Node::Node(), bpp::Node::operator=(), bpp::Node::setDistanceToFather(), and bpp::Node::~Node().
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protectedinherited |
Definition at line 97 of file Node.h.
Referenced by bpp::NodeTemplate< NodeInfos >::getFather(), bpp::Node::getFather(), bpp::Node::getFatherId(), bpp::Node::getNeighbors(), bpp::Node::hasFather(), bpp::NodeTemplate< NodeInfos >::operator[](), bpp::Node::operator[](), bpp::NodeTemplate< NodeInfos >::removeFather(), bpp::Node::removeFather(), and bpp::Node::setFather().
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protectedinherited |
Definition at line 94 of file Node.h.
Referenced by bpp::Node::getId(), bpp::Node::operator=(), bpp::Node::operator==(), and bpp::Node::setId().
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private |
Definition at line 80 of file NodeTemplate.h.
Referenced by bpp::NodeTemplate< NodeInfos >::getInfos(), bpp::NodeTemplate< NodeInfos >::operator=(), and bpp::NodeTemplate< NodeInfos >::setInfos().
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protectedinherited |
Definition at line 95 of file Node.h.
Referenced by bpp::Node::deleteName(), bpp::Node::getName(), bpp::Node::hasName(), bpp::Node::Node(), bpp::Node::operator=(), bpp::Node::setName(), and bpp::Node::~Node().
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mutableprotectedinherited |
Definition at line 99 of file Node.h.
Referenced by bpp::Node::deleteNodeProperties(), bpp::Node::deleteNodeProperty(), bpp::Node::getNodeProperty(), bpp::Node::getNodePropertyNames(), bpp::Node::hasNodeProperty(), bpp::Node::Node(), bpp::Node::operator=(), bpp::Node::removeNodeProperties(), bpp::Node::removeNodeProperty(), bpp::Node::setNodeProperty(), and bpp::Node::~Node().
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protectedinherited |
Definition at line 96 of file Node.h.
Referenced by bpp::Node::addSon(), bpp::Node::getNeighbors(), bpp::Node::getNumberOfSons(), bpp::NodeTemplate< NodeInfos >::getSon(), bpp::Node::getSon(), bpp::Node::getSons(), bpp::Node::getSonsId(), bpp::NodeTemplate< NodeInfos >::operator[](), bpp::Node::operator[](), bpp::Node::removeSon(), bpp::Node::removeSons(), bpp::Node::setFather(), and bpp::Node::setSon().