Defines a Tree Graph Associator. It is a template which follows (subscribed to) a Graph. More...
#include <Bpp/Graph/AssociationTreeGraphObserver.h>
Inheritance diagram for bpp::AssociationTreeGraphObserver< N, E >:
Collaboration diagram for bpp::AssociationTreeGraphObserver< N, E >:
Public Types | |
| typedef AssociationTreeGraphObserver< N, E >::NodeIndex | NodeIndex |
| typedef AssociationTreeGraphObserver< N, E >::EdgeIndex | EdgeIndex |
| typedef TreeGraph::NodeId | NodeGraphid |
| typedef TreeGraph::EdgeId | EdgeGraphid |
| typedef AssociationGraphObserver< N, E >::NodeIterator | NodeIterator |
| typedef AssociationGraphObserver< N, E >::EdgeIterator | EdgeIterator |
Public Member Functions | |
| virtual bool | isValid () const =0 |
| virtual std::shared_ptr< E > | getEdgeToFather (const std::shared_ptr< N > nodeObject) const =0 |
| virtual std::shared_ptr< E > | getEdgeToFather (const NodeIndex nodeIndex) const =0 |
| virtual void | rootAt (const std::shared_ptr< N > root)=0 |
| Sets the root and make the tree directed from root to leaves. More... | |
| virtual bool | isRooted () const =0 |
| virtual std::shared_ptr< N > | getFatherOfNode (const std::shared_ptr< N > nodeObject) const =0 |
| virtual bool | hasFather (const std::shared_ptr< N > nodeObject) const =0 |
| virtual bool | hasFather (const NodeIndex node) const =0 |
| virtual std::vector< std::shared_ptr< N > > | getSons (const std::shared_ptr< N > node) const =0 |
| virtual std::vector< NodeIndex > | getSons (const NodeIndex node) const =0 |
| virtual std::vector< std::shared_ptr< E > > | getBranches (const std::shared_ptr< N > node) const =0 |
| virtual std::vector< EdgeIndex > | getBranches (const NodeIndex node) const =0 |
| virtual std::shared_ptr< N > | getSon (const std::shared_ptr< E > edge) const =0 |
| virtual NodeIndex | getSon (const EdgeIndex edge) const =0 |
| virtual std::shared_ptr< N > | getFatherOfEdge (const std::shared_ptr< E > edge) const =0 |
| virtual NodeIndex | getFatherOfEdge (const EdgeIndex edge) const =0 |
| virtual size_t | getNumberOfSons (const std::shared_ptr< N > node) const =0 |
| virtual std::vector< std::shared_ptr< N > > | getLeavesUnderNode (std::shared_ptr< N > node) const =0 |
| virtual std::vector< std::shared_ptr< N > > | removeSons (const std::shared_ptr< N > node)=0 |
| virtual void | removeSon (const std::shared_ptr< N > node, const std::shared_ptr< N > son)=0 |
| virtual void | setFather (const std::shared_ptr< N > nodeObject, const std::shared_ptr< N > fatherNodeObject, const std::shared_ptr< E > edgeObject=0)=0 |
| virtual void | addSon (const std::shared_ptr< N > nodeObject, const std::shared_ptr< N > sonNodeObject, const std::shared_ptr< E > edgeObject=0)=0 |
| virtual std::unique_ptr< NodeIterator > | sonsIterator (std::shared_ptr< N > node)=0 |
| virtual std::unique_ptr< NodeIterator > | sonsIterator (std::shared_ptr< N > node) const =0 |
| virtual std::unique_ptr< EdgeIterator > | branchesIterator (std::shared_ptr< N > node)=0 |
| virtual std::unique_ptr< EdgeIterator > | branchesIterator (std::shared_ptr< N > node) const =0 |
| virtual std::vector< std::shared_ptr< N > > | getNodePathBetweenTwoNodes (const std::shared_ptr< N > nodeA, const std::shared_ptr< N > nodeB, bool includeAncestor=true) const =0 |
| Get a vector of ancestor nodes between to nodes. More... | |
| virtual std::vector< std::shared_ptr< E > > | getEdgePathBetweenTwoNodes (const std::shared_ptr< N > nodeA, const std::shared_ptr< N > nodeB) const =0 |
| virtual std::vector< std::shared_ptr< N > > | getSubtreeNodes (const std::shared_ptr< N > localRoot) const =0 |
| virtual std::vector< std::shared_ptr< E > > | getSubtreeEdges (const std::shared_ptr< N > localRoot) const =0 |
| virtual Clonable * | clone () const =0 |
| Create a copy of this object and send a pointer to it. More... | |
Graph Relations Management | |
Modificating the structure of the graph. | |
| virtual void | createNode (std::shared_ptr< N > newNodeObject)=0 |
| virtual void | createNode (std::shared_ptr< N > objectOriginNode, std::shared_ptr< N > newNodeObject, std::shared_ptr< E > newEdgeObject=00)=0 |
| virtual void | link (std::shared_ptr< N > nodeObjectA, std::shared_ptr< N > nodeObjectB, std::shared_ptr< E > edgeObject=00)=0 |
| virtual void | unlink (std::shared_ptr< N > nodeObjectA, std::shared_ptr< N > nodeObjectB)=0 |
| virtual void | deleteNode (std::shared_ptr< N > nodeObject)=0 |
Object Association | |
| virtual void | associateNode (std::shared_ptr< N > nodeObject, NodeGraphid node)=0 |
| virtual void | associateEdge (std::shared_ptr< E > edgeObject, EdgeGraphid edge)=0 |
| virtual void | dissociateNode (std::shared_ptr< N > nodeObject)=0 |
| virtual void | dissociateEdge (std::shared_ptr< E > edgeObject)=0 |
| virtual NodeGraphid | getNodeGraphid (const std::shared_ptr< N > nodeObject) const =0 |
| virtual EdgeGraphid | getEdgeGraphid (const std::shared_ptr< E > edgeObject) const =0 |
| virtual const std::shared_ptr< N > | getNodeFromGraphid (NodeGraphid) const =0 |
| virtual std::shared_ptr< N > | getNodeFromGraphid (NodeGraphid)=0 |
| virtual std::vector< std::shared_ptr< N > > | getNodesFromGraphid (std::vector< NodeGraphid >) const =0 |
| virtual std::shared_ptr< E > | getEdgeFromGraphid (EdgeGraphid)=0 |
| virtual const std::shared_ptr< E > | getEdgeFromGraphid (EdgeGraphid) const =0 |
| virtual std::vector< std::shared_ptr< E > > | getEdgesFromGraphid (std::vector< EdgeGraphid >) const =0 |
| virtual std::shared_ptr< N > | getRoot () const =0 |
| virtual NodeIndex | getRootIndex () const =0 |
Object Indexation | |
Get or set indexes to nodes and edges | |
| virtual bool | hasNodeIndex (const std::shared_ptr< N > nodeObject) const =0 |
| return if the object has an index. More... | |
| virtual bool | hasEdgeIndex (const std::shared_ptr< E > edgeObject) const =0 |
| virtual NodeIndex | getNodeIndex (const std::shared_ptr< N > nodeObject) const =0 |
| virtual std::vector< NodeIndex > | getNodeIndexes (std::vector< std::shared_ptr< N >> nodeObjects) const =0 |
| virtual EdgeIndex | getEdgeIndex (const std::shared_ptr< E > edgeObject) const =0 |
| virtual std::vector< EdgeIndex > | getEdgeIndexes (std::vector< std::shared_ptr< E >> edgeObjects) const =0 |
| virtual NodeIndex | setNodeIndex (const std::shared_ptr< N > nodeObject, NodeIndex index)=0 |
| virtual EdgeIndex | setEdgeIndex (const std::shared_ptr< E > edgeObject, EdgeIndex index)=0 |
| virtual bool | hasNode (NodeIndex nodeIndex) const =0 |
| virtual bool | hasEdge (EdgeIndex edgeIndex) const =0 |
| virtual std::shared_ptr< N > | getNode (NodeIndex nodeIndex) const =0 |
| virtual std::shared_ptr< E > | getEdge (EdgeIndex edgeIndex) const =0 |
Iterator interface on Nodes | |
| virtual std::unique_ptr< NodeIterator > | allNodesIterator ()=0 |
| virtual std::unique_ptr< NodeIterator > | allNodesIterator () const =0 |
| virtual std::unique_ptr< NodeIterator > | outgoingNeighborNodesIterator (std::shared_ptr< N > node)=0 |
| virtual std::unique_ptr< NodeIterator > | outgoingNeighborNodesIterator (std::shared_ptr< N > node) const =0 |
| virtual std::unique_ptr< NodeIterator > | incomingNeighborNodesIterator (std::shared_ptr< N > node)=0 |
| virtual std::unique_ptr< NodeIterator > | incomingNeighborNodesIterator (std::shared_ptr< N > node) const =0 |
| virtual std::vector< std::shared_ptr< N > > | getNeighbors (const std::shared_ptr< N > node) const =0 |
| virtual std::vector< NodeIndex > | getNeighbors (NodeIndex node) const =0 |
| virtual std::vector< std::shared_ptr< E > > | getEdges (const std::shared_ptr< N > node) const =0 |
| virtual std::vector< EdgeIndex > | getEdges (NodeIndex node) const =0 |
| virtual std::vector< std::shared_ptr< N > > | getOutgoingNeighbors (const std::shared_ptr< N > node) const =0 |
| virtual std::vector< NodeIndex > | getOutgoingNeighbors (NodeIndex node) const =0 |
| virtual std::vector< std::shared_ptr< E > > | getOutgoingEdges (const std::shared_ptr< N > node) const =0 |
| virtual std::vector< EdgeIndex > | getOutgoingEdges (NodeIndex node) const =0 |
| virtual std::vector< std::shared_ptr< N > > | getIncomingNeighbors (const std::shared_ptr< N > node) const =0 |
| virtual std::vector< NodeIndex > | getIncomingNeighbors (NodeIndex node) const =0 |
| virtual std::vector< std::shared_ptr< E > > | getIncomingEdges (const std::shared_ptr< N > node) const =0 |
| virtual std::vector< EdgeIndex > | getIncomingEdges (NodeIndex node) const =0 |
| virtual std::vector< std::shared_ptr< N > > | getLeavesFromNode (std::shared_ptr< N > node, unsigned int maxDepth) const =0 |
| virtual std::vector< std::shared_ptr< N > > | getAllLeaves () const =0 |
| virtual std::vector< NodeIndex > | getAllLeavesIndexes () const =0 |
| virtual std::vector< std::shared_ptr< N > > | getAllInnerNodes () const =0 |
| virtual std::vector< NodeIndex > | getAllInnerNodesIndexes () const =0 |
| virtual std::vector< std::shared_ptr< N > > | getAllNodes () const =0 |
| virtual std::vector< NodeIndex > | getAllNodesIndexes () const =0 |
Iterator interface on Edges | |
| virtual std::unique_ptr< EdgeIterator > | allEdgesIterator ()=0 |
| virtual std::unique_ptr< EdgeIterator > | outgoingEdgesIterator (std::shared_ptr< N > node)=0 |
| virtual std::unique_ptr< EdgeIterator > | incomingEdgesIterator (std::shared_ptr< N > node)=0 |
| virtual std::vector< std::shared_ptr< E > > | getAllEdges () const =0 |
| virtual std::vector< EdgeIndex > | getAllEdgesIndexes () const =0 |
| virtual std::shared_ptr< E > | getEdgeLinking (std::shared_ptr< N > nodeA, std::shared_ptr< N > nodeB) const =0 |
| virtual void | setEdgeLinking (std::shared_ptr< N > nodeA, std::shared_ptr< N > nodeB, std::shared_ptr< E > edge)=0 |
Function called by the subjectGraph | |
Methods called by the subject graph to make this observer so fit the subject graph | |
| virtual void | deletedEdgesUpdate (const std::vector< unsigned int > &edgesToDelete)=0 |
| virtual void | deletedNodesUpdate (const std::vector< unsigned int > &nodesToDelete)=0 |
Static Public Member Functions | |
| template<class A , class B > | |
| static B * | copy (const A &a, typename std::enable_if< !std::is_base_of< B, A >::value &&!std::is_abstract< B >::value, B *>::type *=0) |
| template<class A , class B > | |
| static B * | copy (const A &a, typename std::enable_if< !std::is_base_of< B, A >::value &&std::is_abstract< B >::value, B *>::type *=0) |
| template<class A , class B > | |
| static B * | copy (const A &a, typename std::enable_if< std::is_base_of< B, A >::value &&!std::is_abstract< A >::value, B *>::type *=0) |
| template<class A , class B > | |
| static B * | copy (const A &a, typename std::enable_if< std::is_base_of< B, A >::value &&std::is_abstract< A >::value &&std::is_base_of< Clonable, A >::value, B *>::type *=0) |
| template<class A , class B > | |
| static B * | copy (const A &a, typename std::enable_if< std::is_base_of< B, A >::value &&std::is_abstract< A >::value &&!std::is_base_of< Clonable, A >::value, B *>::type *=0) |
Detailed Description
template<class N, class E>
class bpp::AssociationTreeGraphObserver< N, E >
Defines a Tree Graph Associator. It is a template which follows (subscribed to) a Graph.
Definition at line 27 of file AssociationTreeGraphObserver.h.
Member Typedef Documentation
◆ EdgeGraphid
| typedef TreeGraph::EdgeId bpp::AssociationTreeGraphObserver< N, E >::EdgeGraphid |
Definition at line 35 of file AssociationTreeGraphObserver.h.
◆ EdgeIndex
| typedef AssociationTreeGraphObserver<N, E>::EdgeIndex bpp::AssociationTreeGraphObserver< N, E >::EdgeIndex |
Definition at line 32 of file AssociationTreeGraphObserver.h.
◆ EdgeIterator
| typedef AssociationGraphObserver<N, E>::EdgeIterator bpp::AssociationTreeGraphObserver< N, E >::EdgeIterator |
Definition at line 183 of file AssociationTreeGraphObserver.h.
◆ NodeGraphid
| typedef TreeGraph::NodeId bpp::AssociationTreeGraphObserver< N, E >::NodeGraphid |
Definition at line 34 of file AssociationTreeGraphObserver.h.
◆ NodeIndex
| typedef AssociationTreeGraphObserver<N, E>::NodeIndex bpp::AssociationTreeGraphObserver< N, E >::NodeIndex |
Definition at line 31 of file AssociationTreeGraphObserver.h.
◆ NodeIterator
| typedef AssociationGraphObserver<N, E>::NodeIterator bpp::AssociationTreeGraphObserver< N, E >::NodeIterator |
Iterators
Definition at line 182 of file AssociationTreeGraphObserver.h.
Member Function Documentation
◆ addSon()
|
pure virtual |
Add a son to a node
- Parameters
-
nodeObject the concerned node sonNodeObject the node to be added as a son to the father edgeObject the optional edge between the nodes (default = 00)
Implemented in bpp::AssociationTreeGraphImplObserver< N, E, TreeGraphImpl >.
◆ allEdgesIterator()
|
pure virtualinherited |
◆ allNodesIterator() [1/2]
|
pure virtualinherited |
◆ allNodesIterator() [2/2]
|
pure virtualinherited |
◆ associateEdge()
|
pure virtualinherited |
Associate a E object to an edge in the graph.
- Parameters
-
edgeObject object to associate edge existing edge to be associated
Implemented in bpp::AssociationGraphImplObserver< N, E, GraphImpl >, bpp::AssociationGraphImplObserver< N, E, DAGraphImpl >, and bpp::AssociationGraphImplObserver< N, E, TreeGraphImpl >.
Referenced by bpp::AssociationGraphObserver< N, E >::copy().
◆ associateNode()
|
pure virtualinherited |
Associate a N object to a node in the graph.
- Parameters
-
nodeObject object to associate node existing node to be associated
Implemented in bpp::AssociationGraphImplObserver< N, E, GraphImpl >, bpp::AssociationGraphImplObserver< N, E, DAGraphImpl >, and bpp::AssociationGraphImplObserver< N, E, TreeGraphImpl >.
Referenced by bpp::AssociationGraphObserver< N, E >::copy().
◆ branchesIterator() [1/2]
|
pure virtual |
Implemented in bpp::AssociationTreeGraphImplObserver< N, E, TreeGraphImpl >.
◆ branchesIterator() [2/2]
|
pure virtual |
Implemented in bpp::AssociationTreeGraphImplObserver< N, E, TreeGraphImpl >.
◆ clone()
|
pure virtualinherited |
Create a copy of this object and send a pointer to it.
- Returns
- A pointer toward the copy object.
Implemented in bpp::TestFunction, bpp::InfinityDerivableSecondOrderWrapper, bpp::InfinityDerivableFirstOrderWrapper, bpp::InfinityFunctionWrapper, bpp::LinearMatrix< Scalar >, bpp::AssociationGraphImplObserver< N, E, GraphImpl >, bpp::AssociationGraphImplObserver< N, E, DAGraphImpl >, bpp::AssociationGraphImplObserver< N, E, TreeGraphImpl >, bpp::StdErr, bpp::FunctionStopCondition, bpp::ColMatrix< Scalar >, bpp::PlaceboTransformedParameter, bpp::StdOut, bpp::GlobalGraph, bpp::ParametersStopCondition, bpp::StlOutputStreamWrapper, bpp::ReparametrizationDerivableSecondOrderWrapper, bpp::IntervalTransformedParameter, bpp::MetaOptimizer, bpp::IntervalConstraint, bpp::BppUnsignedInteger, bpp::StlOutputStream, bpp::SecondOrderDerivable, bpp::LogsumHmmLikelihood, bpp::RescaledHmmLikelihood, bpp::ReparametrizationDerivableFirstOrderWrapper, bpp::BppInteger, bpp::RowMatrix< Scalar >, bpp::RowMatrix< double >, bpp::RowMatrix< Real >, bpp::Parameter, bpp::Simplex, bpp::LowMemoryRescaledHmmLikelihood, bpp::Table< T >, bpp::AbstractNumericalDerivative, bpp::BppDouble, bpp::RTransformedParameter, bpp::NullOutputStream, bpp::ParametrizableCollection< N >, bpp::FirstOrderDerivable, bpp::OptimizerInterface, bpp::AssociationTreeGraphImplObserver< N, E, TreeGraphImpl >, bpp::AssociationDAGraphImplObserver< N, E, DAGraphImpl >, bpp::ThreePointsNumericalDerivative, bpp::DirichletDiscreteDistribution, bpp::SimpleDiscreteDistribution, bpp::DownhillSimplexMethod, bpp::Number< T >, bpp::Number< double >, bpp::Number< int >, bpp::Number< unsigned int >, bpp::FivePointsNumericalDerivative, bpp::ReparametrizationFunctionWrapper, bpp::DataTable, bpp::PrincipalComponentAnalysis, bpp::DualityDiagram, bpp::TruncatedExponentialDiscreteDistribution, bpp::MetaOptimizerInfos, bpp::BrentOneDimension, bpp::NewtonBacktrackOneDimension, bpp::FunctionOperator< F >, bpp::AutoParameter, bpp::GammaDiscreteDistribution, bpp::MixtureOfDiscreteDistributions, bpp::AliasParameterListener, bpp::Range< T >, bpp::PowellMultiDimensions, bpp::InvariantMixedDiscreteDistribution, bpp::TwoPointsNumericalDerivative, bpp::ParameterListener, bpp::OutputStream, bpp::GoldenSectionSearch, bpp::DirectionFunction, bpp::Point2D< T >, bpp::BetaDiscreteDistribution, bpp::ExponentialDiscreteDistribution, bpp::ParameterList, bpp::CorrespondenceAnalysis, bpp::HmmLikelihood, bpp::GaussianDiscreteDistribution, bpp::BfgsMultiDimensions, bpp::NewtonBacktrackOneDimension::NBODStopCondition, bpp::FullHmmTransitionMatrix, bpp::BppNotANumber, bpp::UniformDiscreteDistribution, bpp::ContingencyTableTest, bpp::Font, bpp::ConstantDistribution, bpp::DiscreteDistributionInterface, bpp::MultipleDiscreteDistribution, bpp::DownhillSimplexMethod::DSMStopCondition, bpp::MathOperator, bpp::BrentOneDimension::BODStopCondition, bpp::ConjugateGradientMultiDimensions, bpp::OptimizationStopCondition, bpp::AutoCorrelationTransitionMatrix, bpp::ParameterEvent, bpp::ComputationTree, bpp::GoldenSectionSearch::GSSStopCondition, bpp::PowellMultiDimensions::PMDStopCondition, bpp::ConstraintInterface, bpp::HmmStateAlphabet, bpp::RGBColor, bpp::SimpleMultiDimensions, bpp::SimpleNewtonMultiDimensions, bpp::HmmEmissionProbabilities, bpp::BinaryOperator, bpp::BppVector< T >, bpp::TransformedParameter, bpp::BppString, bpp::ConstantOperator, bpp::NegativeOperator, bpp::HmmTransitionMatrix, bpp::BppNumberI, bpp::BppBoolean, and bpp::NewtonOneDimension.
Referenced by bpp::FirstOrderDerivable::~FirstOrderDerivable(), and bpp::SecondOrderDerivable::~SecondOrderDerivable().
◆ copy() [1/5]
|
inlinestaticinherited |
Specific copy of A and B objects, if clonable or not.
Definition at line 45 of file AssociationGraphObserver.h.
◆ copy() [2/5]
|
inlinestaticinherited |
Definition at line 51 of file AssociationGraphObserver.h.
◆ copy() [3/5]
|
inlinestaticinherited |
Definition at line 58 of file AssociationGraphObserver.h.
◆ copy() [4/5]
|
inlinestaticinherited |
Definition at line 64 of file AssociationGraphObserver.h.
◆ copy() [5/5]
|
inlinestaticinherited |
Definition at line 70 of file AssociationGraphObserver.h.
References bpp::AssociationGraphObserver< N, E >::associateEdge(), bpp::AssociationGraphObserver< N, E >::associateNode(), bpp::AssociationGraphObserver< N, E >::createNode(), bpp::AssociationGraphObserver< N, E >::deleteNode(), bpp::AssociationGraphObserver< N, E >::dissociateEdge(), bpp::AssociationGraphObserver< N, E >::dissociateNode(), bpp::AssociationGraphObserver< N, E >::getEdge(), bpp::AssociationGraphObserver< N, E >::getEdgeFromGraphid(), bpp::AssociationGraphObserver< N, E >::getEdgeGraphid(), bpp::AssociationGraphObserver< N, E >::getEdgeIndex(), bpp::AssociationGraphObserver< N, E >::getEdgeIndexes(), bpp::AssociationGraphObserver< N, E >::getEdgesFromGraphid(), bpp::AssociationGraphObserver< N, E >::getNode(), bpp::AssociationGraphObserver< N, E >::getNodeFromGraphid(), bpp::AssociationGraphObserver< N, E >::getNodeGraphid(), bpp::AssociationGraphObserver< N, E >::getNodeIndex(), bpp::AssociationGraphObserver< N, E >::getNodeIndexes(), bpp::AssociationGraphObserver< N, E >::getNodesFromGraphid(), bpp::AssociationGraphObserver< N, E >::getRoot(), bpp::AssociationGraphObserver< N, E >::getRootIndex(), bpp::AssociationGraphObserver< N, E >::hasEdge(), bpp::AssociationGraphObserver< N, E >::hasEdgeIndex(), bpp::AssociationGraphObserver< N, E >::hasNode(), bpp::AssociationGraphObserver< N, E >::hasNodeIndex(), bpp::AssociationGraphObserver< N, E >::link(), bpp::AssociationGraphObserver< N, E >::setEdgeIndex(), bpp::AssociationGraphObserver< N, E >::setNodeIndex(), and bpp::AssociationGraphObserver< N, E >::unlink().
◆ createNode() [1/2]
|
pure virtualinherited |
Creates an orphaned node from a NodeClass object.
- Parameters
-
newNodeObject the N object associated to the node in the graph.
Implemented in bpp::AssociationGraphImplObserver< N, E, GraphImpl >, bpp::AssociationGraphImplObserver< N, E, DAGraphImpl >, and bpp::AssociationGraphImplObserver< N, E, TreeGraphImpl >.
Referenced by bpp::AssociationGraphObserver< N, E >::copy().
◆ createNode() [2/2]
|
pure virtualinherited |
Creates an node linked to an existing node. Order of parameters match the link method.
- Parameters
-
newNodeObject the N object associated to the node in the graph. objectOriginNode existing node. In a directed graph: origin -> newNode. newEdgeObject optional edge between nodes (default = 00)
Implemented in bpp::AssociationGraphImplObserver< N, E, GraphImpl >, bpp::AssociationGraphImplObserver< N, E, DAGraphImpl >, and bpp::AssociationGraphImplObserver< N, E, TreeGraphImpl >.
◆ deletedEdgesUpdate()
|
pure virtualinherited |
Delete unused object edges, since they have been deleted in the graph
- Parameters
-
edgesToDelete a vector of Edges to delete
Implemented in bpp::AssociationGraphImplObserver< N, E, GraphImpl >, bpp::AssociationGraphImplObserver< N, E, DAGraphImpl >, and bpp::AssociationGraphImplObserver< N, E, TreeGraphImpl >.
◆ deletedNodesUpdate()
|
pure virtualinherited |
Delete unused object nodes, since they have been deleted in the graph
- Parameters
-
nodesToDelete a vector of N to delete
Implemented in bpp::AssociationGraphImplObserver< N, E, GraphImpl >, bpp::AssociationGraphImplObserver< N, E, DAGraphImpl >, and bpp::AssociationGraphImplObserver< N, E, TreeGraphImpl >.
◆ deleteNode()
|
pure virtualinherited |
Deletes a node
- Parameters
-
nodeObject node to be deleted
Implemented in bpp::AssociationGraphImplObserver< N, E, GraphImpl >, bpp::AssociationGraphImplObserver< N, E, DAGraphImpl >, and bpp::AssociationGraphImplObserver< N, E, TreeGraphImpl >.
Referenced by bpp::AssociationGraphObserver< N, E >::copy().
◆ dissociateEdge()
|
pure virtualinherited |
◆ dissociateNode()
|
pure virtualinherited |
Dissociate a N or E object to a node or an edge in the graph. Graph is not changed.
- Parameters
-
nodeObject object to dissociate
Implemented in bpp::AssociationGraphImplObserver< N, E, GraphImpl >, bpp::AssociationGraphImplObserver< N, E, DAGraphImpl >, and bpp::AssociationGraphImplObserver< N, E, TreeGraphImpl >.
Referenced by bpp::AssociationGraphObserver< N, E >::copy().
◆ getAllEdges()
|
pure virtualinherited |
Get all the defined edges of a graphO,
- Returns
- a vector containing the branchesObjects
Implemented in bpp::AssociationGraphImplObserver< N, E, GraphImpl >, bpp::AssociationGraphImplObserver< N, E, DAGraphImpl >, and bpp::AssociationGraphImplObserver< N, E, TreeGraphImpl >.
Referenced by bpp::AssociationGraphObserver< N, E >::EdgeIterator::~EdgeIterator().
◆ getAllEdgesIndexes()
|
pure virtualinherited |
◆ getAllInnerNodes()
|
pure virtualinherited |
Get all the inner nodes of a graph, ie, nodes with degree >= 2.
- Returns
- a vector containing the inner nodes.
Implemented in bpp::AssociationGraphImplObserver< N, E, GraphImpl >, bpp::AssociationGraphImplObserver< N, E, DAGraphImpl >, and bpp::AssociationGraphImplObserver< N, E, TreeGraphImpl >.
Referenced by bpp::AssociationGraphObserver< N, E >::NodeIterator::~NodeIterator().
◆ getAllInnerNodesIndexes()
|
pure virtualinherited |
◆ getAllLeaves()
|
pure virtualinherited |
Get all the leaves objects of a graph, ie, nodes with only one neighbor,
- Returns
- a vector containing the leaves
Implemented in bpp::AssociationGraphImplObserver< N, E, GraphImpl >, bpp::AssociationGraphImplObserver< N, E, DAGraphImpl >, and bpp::AssociationGraphImplObserver< N, E, TreeGraphImpl >.
Referenced by bpp::AssociationGraphObserver< N, E >::NodeIterator::~NodeIterator().
◆ getAllLeavesIndexes()
|
pure virtualinherited |
◆ getAllNodes()
|
pure virtualinherited |
Get all the defined nodes of a graphO,
- Returns
- a vector containing the nodesObjects
Implemented in bpp::AssociationGraphImplObserver< N, E, GraphImpl >, bpp::AssociationGraphImplObserver< N, E, DAGraphImpl >, and bpp::AssociationGraphImplObserver< N, E, TreeGraphImpl >.
Referenced by bpp::AssociationGraphObserver< N, E >::NodeIterator::~NodeIterator().
◆ getAllNodesIndexes()
|
pure virtualinherited |
◆ getBranches() [1/2]
|
pure virtual |
Return the branches to the sons of a node
- Parameters
-
node the concerned node
- Returns
- a vector of branch Nodes
Implemented in bpp::AssociationTreeGraphImplObserver< N, E, TreeGraphImpl >.
◆ getBranches() [2/2]
|
pure virtual |
Implemented in bpp::AssociationTreeGraphImplObserver< N, E, TreeGraphImpl >.
◆ getEdge()
|
pure virtualinherited |
Return the associated Node index
- Parameters
-
edgeIndex the index of the wanted edge
- Returns
- E, an edge object
Implemented in bpp::AssociationGraphImplObserver< N, E, GraphImpl >, bpp::AssociationGraphImplObserver< N, E, DAGraphImpl >, and bpp::AssociationGraphImplObserver< N, E, TreeGraphImpl >.
Referenced by bpp::AssociationGraphObserver< N, E >::copy().
◆ getEdgeFromGraphid() [1/2]
|
pure virtualinherited |
◆ getEdgeFromGraphid() [2/2]
|
pure virtualinherited |
◆ getEdgeGraphid()
|
pure virtualinherited |
Return the associated Node ID
- Parameters
-
edgeObject object which to return the node ID
- Returns
- a node ID
Implemented in bpp::AssociationGraphImplObserver< N, E, GraphImpl >, bpp::AssociationGraphImplObserver< N, E, DAGraphImpl >, and bpp::AssociationGraphImplObserver< N, E, TreeGraphImpl >.
Referenced by bpp::AssociationGraphObserver< N, E >::copy().
◆ getEdgeIndex()
|
pure virtualinherited |
Return the associated Node index
- Parameters
-
edgeObject object which to return the node index
- Returns
- a node index
Implemented in bpp::AssociationGraphImplObserver< N, E, GraphImpl >, bpp::AssociationGraphImplObserver< N, E, DAGraphImpl >, and bpp::AssociationGraphImplObserver< N, E, TreeGraphImpl >.
Referenced by bpp::AssociationGraphObserver< N, E >::copy().
◆ getEdgeIndexes()
|
pure virtualinherited |
Referenced by bpp::AssociationGraphObserver< N, E >::copy().
◆ getEdgeLinking()
|
pure virtualinherited |
Returns the Edge between two nodes nodeA -> nodeB
- Parameters
-
nodeA source node (if directed) nodeB destination node (if directed)
- Returns
- the edge between these two nodes
Implemented in bpp::AssociationGraphImplObserver< N, E, GraphImpl >, bpp::AssociationGraphImplObserver< N, E, DAGraphImpl >, and bpp::AssociationGraphImplObserver< N, E, TreeGraphImpl >.
Referenced by bpp::AssociationGraphObserver< N, E >::EdgeIterator::~EdgeIterator().
◆ getEdgePathBetweenTwoNodes()
|
pure virtual |
Implemented in bpp::AssociationTreeGraphImplObserver< N, E, TreeGraphImpl >.
◆ getEdges() [1/2]
|
pure virtualinherited |
Get all the edges from/to a node in the graph.
- Parameters
-
node the node one wants to get its neighbor edges
- Returns
- a vector containing the edges
Implemented in bpp::AssociationGraphImplObserver< N, E, GraphImpl >, bpp::AssociationGraphImplObserver< N, E, DAGraphImpl >, and bpp::AssociationGraphImplObserver< N, E, TreeGraphImpl >.
Referenced by bpp::AssociationGraphObserver< N, E >::NodeIterator::~NodeIterator().
◆ getEdges() [2/2]
|
pure virtualinherited |
◆ getEdgesFromGraphid()
|
pure virtualinherited |
◆ getEdgeToFather() [1/2]
|
pure virtual |
Return, in a rooted tree, the branch leading to the father
- Parameters
-
nodeObject the concerned node
- Returns
- an Edge which is the branch to the father
Implemented in bpp::AssociationTreeGraphImplObserver< N, E, TreeGraphImpl >.
◆ getEdgeToFather() [2/2]
|
pure virtual |
Implemented in bpp::AssociationTreeGraphImplObserver< N, E, TreeGraphImpl >.
◆ getFatherOfEdge() [1/2]
|
pure virtual |
Return, in a rooted tree, the father of an edge
- Parameters
-
edge the concerned edge
- Returns
- the father Node
Implemented in bpp::AssociationTreeGraphImplObserver< N, E, TreeGraphImpl >.
◆ getFatherOfEdge() [2/2]
|
pure virtual |
Implemented in bpp::AssociationTreeGraphImplObserver< N, E, TreeGraphImpl >.
◆ getFatherOfNode()
|
pure virtual |
Return, in a rooted tree, the father node
- Parameters
-
nodeObject the concerned node
- Returns
- the father
Implemented in bpp::AssociationTreeGraphImplObserver< N, E, TreeGraphImpl >.
◆ getIncomingEdges() [1/2]
|
pure virtualinherited |
In an directed graph, get all the edges which are coming to a node in the graph.
- Parameters
-
node the node one wants to get its edges
- Returns
- a vector containing the incoming edges
Implemented in bpp::AssociationGraphImplObserver< N, E, GraphImpl >, bpp::AssociationGraphImplObserver< N, E, DAGraphImpl >, and bpp::AssociationGraphImplObserver< N, E, TreeGraphImpl >.
Referenced by bpp::AssociationGraphObserver< N, E >::NodeIterator::~NodeIterator().
◆ getIncomingEdges() [2/2]
|
pure virtualinherited |
◆ getIncomingNeighbors() [1/2]
|
pure virtualinherited |
In an directed graph, get all the neighbors which are coming to a node in the graph.
- Parameters
-
node the node one wants to get its neighbors
- Returns
- a vector containing the incoming neighbors
Implemented in bpp::AssociationGraphImplObserver< N, E, GraphImpl >, bpp::AssociationGraphImplObserver< N, E, DAGraphImpl >, and bpp::AssociationGraphImplObserver< N, E, TreeGraphImpl >.
Referenced by bpp::AssociationGraphObserver< N, E >::NodeIterator::~NodeIterator().
◆ getIncomingNeighbors() [2/2]
|
pure virtualinherited |
◆ getLeavesFromNode()
|
pure virtualinherited |
Get the leaves of a graph, ie, nodes with only one neighbor, starting from a peculiar node, up to a specific depth.
- Parameters
-
node the starting node maxDepth the max recursion depth
- Returns
- a vector containing the leaves
Implemented in bpp::AssociationGraphImplObserver< N, E, GraphImpl >, bpp::AssociationGraphImplObserver< N, E, DAGraphImpl >, and bpp::AssociationGraphImplObserver< N, E, TreeGraphImpl >.
Referenced by bpp::AssociationGraphObserver< N, E >::NodeIterator::~NodeIterator().
◆ getLeavesUnderNode()
|
pure virtual |
Get the leaves of a tree under a peculiar node.
- Parameters
-
node the starting node
- Returns
- a vector containing the leaves
Implemented in bpp::AssociationTreeGraphImplObserver< N, E, TreeGraphImpl >.
◆ getNeighbors() [1/2]
|
pure virtualinherited |
Get all the neighbors of a node in the graph.
- Parameters
-
node the node one wants to get its neighbors
- Returns
- a vector containing the neighbors
Implemented in bpp::AssociationGraphImplObserver< N, E, GraphImpl >, bpp::AssociationGraphImplObserver< N, E, DAGraphImpl >, and bpp::AssociationGraphImplObserver< N, E, TreeGraphImpl >.
Referenced by bpp::AssociationGraphObserver< N, E >::NodeIterator::~NodeIterator().
◆ getNeighbors() [2/2]
|
pure virtualinherited |
◆ getNode()
|
pure virtualinherited |
Return the associated Node, querying with an index
- Parameters
-
nodeIndex the index of the wanted node
- Returns
- N, a node object
Implemented in bpp::AssociationGraphImplObserver< N, E, GraphImpl >, bpp::AssociationGraphImplObserver< N, E, DAGraphImpl >, and bpp::AssociationGraphImplObserver< N, E, TreeGraphImpl >.
Referenced by bpp::AssociationGraphObserver< N, E >::copy().
◆ getNodeFromGraphid() [1/2]
|
pure virtualinherited |
Transforms an (a list of) id(s) into an (a list of) object(s)
Implemented in bpp::AssociationGraphImplObserver< N, E, GraphImpl >, bpp::AssociationGraphImplObserver< N, E, DAGraphImpl >, and bpp::AssociationGraphImplObserver< N, E, TreeGraphImpl >.
Referenced by bpp::AssociationGraphObserver< N, E >::copy().
◆ getNodeFromGraphid() [2/2]
|
pure virtualinherited |
◆ getNodeGraphid()
|
pure virtualinherited |
Return the associated Node ID
- Parameters
-
nodeObject object which to return the node ID
- Returns
- a node ID
Implemented in bpp::AssociationGraphImplObserver< N, E, GraphImpl >, bpp::AssociationGraphImplObserver< N, E, DAGraphImpl >, and bpp::AssociationGraphImplObserver< N, E, TreeGraphImpl >.
Referenced by bpp::AssociationGraphObserver< N, E >::copy().
◆ getNodeIndex()
|
pure virtualinherited |
Return the associated Node index
- Parameters
-
nodeObject object which to return the node index
- Returns
- a node index
Implemented in bpp::AssociationGraphImplObserver< N, E, GraphImpl >, bpp::AssociationGraphImplObserver< N, E, DAGraphImpl >, and bpp::AssociationGraphImplObserver< N, E, TreeGraphImpl >.
Referenced by bpp::AssociationGraphObserver< N, E >::copy().
◆ getNodeIndexes()
|
pure virtualinherited |
Referenced by bpp::AssociationGraphObserver< N, E >::copy().
◆ getNodePathBetweenTwoNodes()
|
pure virtual |
Get a vector of ancestor nodes between to nodes.
- Parameters
-
nodeA first node. nodeB second node. includeAncestor Tell if the common ancestor must be included in the vector.
- Returns
- A vector of ancestor nodes ids.
- Exceptions
-
PhyloNodeNotFoundException If a node is not found.
Implemented in bpp::AssociationTreeGraphImplObserver< N, E, TreeGraphImpl >.
◆ getNodesFromGraphid()
|
pure virtualinherited |
◆ getNumberOfSons()
|
pure virtual |
Return, in a rooted tree, the number of sons
- Parameters
-
node the concerned node
- Returns
- the number of sons
Implemented in bpp::AssociationTreeGraphImplObserver< N, E, TreeGraphImpl >.
◆ getOutgoingEdges() [1/2]
|
pure virtualinherited |
In an directed graph, get all the edges which are leaving a node in the graph.
- Parameters
-
node the node one wants to get its edges
- Returns
- a vector containing the outgoing edges
Implemented in bpp::AssociationGraphImplObserver< N, E, GraphImpl >, bpp::AssociationGraphImplObserver< N, E, DAGraphImpl >, and bpp::AssociationGraphImplObserver< N, E, TreeGraphImpl >.
Referenced by bpp::AssociationGraphObserver< N, E >::NodeIterator::~NodeIterator().
◆ getOutgoingEdges() [2/2]
|
pure virtualinherited |
◆ getOutgoingNeighbors() [1/2]
|
pure virtualinherited |
In an directed graph, get all the neighbors which are leaving a node in the graph.
- Parameters
-
node the node one wants to get its neighbors
- Returns
- a vector containing the outgoing neighbors
Implemented in bpp::AssociationGraphImplObserver< N, E, GraphImpl >, bpp::AssociationGraphImplObserver< N, E, DAGraphImpl >, and bpp::AssociationGraphImplObserver< N, E, TreeGraphImpl >.
Referenced by bpp::AssociationGraphObserver< N, E >::NodeIterator::~NodeIterator().
◆ getOutgoingNeighbors() [2/2]
|
pure virtualinherited |
◆ getRoot()
|
pure virtualinherited |
- Returns
- the root
Implemented in bpp::AssociationGraphImplObserver< N, E, GraphImpl >, bpp::AssociationGraphImplObserver< N, E, DAGraphImpl >, and bpp::AssociationGraphImplObserver< N, E, TreeGraphImpl >.
Referenced by bpp::AssociationGraphObserver< N, E >::copy().
◆ getRootIndex()
|
pure virtualinherited |
◆ getSon() [1/2]
|
pure virtual |
Return, in a rooted tree, the son of an edge
- Parameters
-
edge the concerned edge
- Returns
- the son Node
Implemented in bpp::AssociationTreeGraphImplObserver< N, E, TreeGraphImpl >.
◆ getSon() [2/2]
|
pure virtual |
Implemented in bpp::AssociationTreeGraphImplObserver< N, E, TreeGraphImpl >.
◆ getSons() [1/2]
|
pure virtual |
Return, in a rooted tree, the sons of a node
- Parameters
-
node the concerned node
- Returns
- a vector of son Nodes
Implemented in bpp::AssociationTreeGraphImplObserver< N, E, TreeGraphImpl >.
◆ getSons() [2/2]
|
pure virtual |
Implemented in bpp::AssociationTreeGraphImplObserver< N, E, TreeGraphImpl >.
◆ getSubtreeEdges()
|
pure virtual |
Implemented in bpp::AssociationTreeGraphImplObserver< N, E, TreeGraphImpl >.
◆ getSubtreeNodes()
|
pure virtual |
Implemented in bpp::AssociationTreeGraphImplObserver< N, E, TreeGraphImpl >.
◆ hasEdge()
|
pure virtualinherited |
Return if the Graph has an edge matching edgeIndex
- Parameters
-
edgeIndex the index of the wanted edge
Implemented in bpp::AssociationGraphImplObserver< N, E, GraphImpl >, bpp::AssociationGraphImplObserver< N, E, DAGraphImpl >, and bpp::AssociationGraphImplObserver< N, E, TreeGraphImpl >.
Referenced by bpp::AssociationGraphObserver< N, E >::copy().
◆ hasEdgeIndex()
|
pure virtualinherited |
◆ hasFather() [1/2]
|
pure virtual |
Has the node a father?
Implemented in bpp::AssociationTreeGraphImplObserver< N, E, TreeGraphImpl >.
◆ hasFather() [2/2]
|
pure virtual |
Implemented in bpp::AssociationTreeGraphImplObserver< N, E, TreeGraphImpl >.
◆ hasNode()
|
pure virtualinherited |
Return if the Graph has a node matching nodeIndex
- Parameters
-
nodeIndex the index of the wanted node
Implemented in bpp::AssociationGraphImplObserver< N, E, GraphImpl >, bpp::AssociationGraphImplObserver< N, E, DAGraphImpl >, and bpp::AssociationGraphImplObserver< N, E, TreeGraphImpl >.
Referenced by bpp::AssociationGraphObserver< N, E >::copy().
◆ hasNodeIndex()
|
pure virtualinherited |
return if the object has an index.
Implemented in bpp::AssociationGraphImplObserver< N, E, GraphImpl >, bpp::AssociationGraphImplObserver< N, E, DAGraphImpl >, and bpp::AssociationGraphImplObserver< N, E, TreeGraphImpl >.
Referenced by bpp::AssociationGraphObserver< N, E >::copy().
◆ incomingEdgesIterator()
|
pure virtualinherited |
◆ incomingNeighborNodesIterator() [1/2]
|
pure virtualinherited |
◆ incomingNeighborNodesIterator() [2/2]
|
pure virtualinherited |
◆ isRooted()
|
pure virtual |
Implemented in bpp::AssociationTreeGraphImplObserver< N, E, TreeGraphImpl >.
◆ isValid()
|
pure virtual |
Is the graph a tree? A tree must be acyclic and with no isolated node.
- Returns
- true if valid tree
Implemented in bpp::AssociationTreeGraphImplObserver< N, E, TreeGraphImpl >.
◆ link()
|
pure virtualinherited |
Creates a link between two existing nodes. If directed graph: nodeA -> nodeB.
- Parameters
-
nodeObjectA source node (or first node if undirected) nodeObjectB target node (or second node if undirected) edgeObject the optional edge between the nodes (default = 00)
Implemented in bpp::AssociationGraphImplObserver< N, E, GraphImpl >, bpp::AssociationGraphImplObserver< N, E, DAGraphImpl >, and bpp::AssociationGraphImplObserver< N, E, TreeGraphImpl >.
Referenced by bpp::AssociationGraphObserver< N, E >::copy().
◆ outgoingEdgesIterator()
|
pure virtualinherited |
◆ outgoingNeighborNodesIterator() [1/2]
|
pure virtualinherited |
◆ outgoingNeighborNodesIterator() [2/2]
|
pure virtualinherited |
◆ removeSon()
|
pure virtual |
Remove a son of a node
Implemented in bpp::AssociationTreeGraphImplObserver< N, E, TreeGraphImpl >.
◆ removeSons()
|
pure virtual |
Remove the sons of a node
- Returns
- a vector containing the removed nodes
Implemented in bpp::AssociationTreeGraphImplObserver< N, E, TreeGraphImpl >.
◆ rootAt()
|
pure virtual |
Sets the root and make the tree directed from root to leaves.
Implemented in bpp::AssociationTreeGraphImplObserver< N, E, TreeGraphImpl >.
◆ setEdgeIndex()
|
pure virtualinherited |
Set an index associated to an edge
- Parameters
-
edgeObject object to which one want to set the index index intex to be given, 0 to get the first free index
- Returns
- the given index
Implemented in bpp::AssociationGraphImplObserver< N, E, GraphImpl >, bpp::AssociationGraphImplObserver< N, E, DAGraphImpl >, and bpp::AssociationGraphImplObserver< N, E, TreeGraphImpl >.
Referenced by bpp::AssociationGraphObserver< N, E >::copy().
◆ setEdgeLinking()
|
pure virtualinherited |
Sets the Edge between two nodes nodeA -> nodeB
- Parameters
-
nodeA source node (if directed) nodeB destination node (if directed) edge the edge between these two nodes
Implemented in bpp::AssociationGraphImplObserver< N, E, GraphImpl >, bpp::AssociationGraphImplObserver< N, E, DAGraphImpl >, and bpp::AssociationGraphImplObserver< N, E, TreeGraphImpl >.
Referenced by bpp::AssociationGraphObserver< N, E >::EdgeIterator::~EdgeIterator().
◆ setFather()
|
pure virtual |
Change / set the father of a node
- Parameters
-
nodeObject the concerned node fatherNodeObject the node to be the father edgeObject the optional edge between the nodes (default = 00)
Implemented in bpp::AssociationTreeGraphImplObserver< N, E, TreeGraphImpl >.
◆ setNodeIndex()
|
pure virtualinherited |
Set an index associated to a node
- Parameters
-
nodeObject object to which one want to set the index index intex to be given, 0 to get the first free index
- Returns
- the given index
Implemented in bpp::AssociationGraphImplObserver< N, E, GraphImpl >, bpp::AssociationGraphImplObserver< N, E, DAGraphImpl >, and bpp::AssociationGraphImplObserver< N, E, TreeGraphImpl >.
Referenced by bpp::AssociationGraphObserver< N, E >::copy().
◆ sonsIterator() [1/2]
|
pure virtual |
Implemented in bpp::AssociationTreeGraphImplObserver< N, E, TreeGraphImpl >.
◆ sonsIterator() [2/2]
|
pure virtual |
Implemented in bpp::AssociationTreeGraphImplObserver< N, E, TreeGraphImpl >.
◆ unlink()
|
pure virtualinherited |
Detroys a link between two existing nodes in the graph. If directed graph: nodeA -> nodeB.
- Parameters
-
nodeObjectA source node (or first node if undirected) nodeObjectB target node (or second node if undirected)
Implemented in bpp::AssociationGraphImplObserver< N, E, GraphImpl >, bpp::AssociationGraphImplObserver< N, E, DAGraphImpl >, and bpp::AssociationGraphImplObserver< N, E, TreeGraphImpl >.
Referenced by bpp::AssociationGraphObserver< N, E >::copy().
The documentation for this class was generated from the following file:
- Bpp/Graph/AssociationTreeGraphObserver.h
