| AbstractSinglePhyloSubstitutionMapping(std::shared_ptr< TreeGlobalGraph > graph, std::shared_ptr< const SubstitutionRegisterInterface > reg, std::shared_ptr< const AlphabetIndex2 > weights, std::shared_ptr< const AlphabetIndex2 > distances) | bpp::AbstractSinglePhyloSubstitutionMapping | inline |
| AbstractSinglePhyloSubstitutionMapping(const AbstractSinglePhyloSubstitutionMapping &sppm) | bpp::AbstractSinglePhyloSubstitutionMapping | |
| addEdgeIndex(const Eref edgeObject) | bpp::AssociationTreeGraphImplObserver< class, class, class > | |
| addEdgeIndex(const Eref edgeObject) | bpp::AssociationTreeGraphImplObserver< class, class, class > | |
| addModel(size_t index, const TransitionModelInterface &model, Vuint brIds) | bpp::AbstractSinglePhyloSubstitutionMapping | |
| addNodeIndex(const Nref nodeObject) | bpp::AssociationTreeGraphImplObserver< class, class, class > | |
| addNodeIndex(const Nref nodeObject) | bpp::AssociationTreeGraphImplObserver< class, class, class > | |
| addSon(const std::shared_ptr< N > nodeObject, const std::shared_ptr< N > sonNodeObject, const std::shared_ptr< E > edgeObject=0) | bpp::AssociationTreeGraphImplObserver< class, class, class > | virtual |
| allEdgesIterator()=0 | bpp::AssociationTreeGraphImplObserver< class, class, class > | pure virtual |
| allEdgesIterator() | bpp::AssociationTreeGraphImplObserver< class, class, class > | virtual |
| allEdgesIterator() const | bpp::AssociationTreeGraphImplObserver< class, class, class > | |
| allEdgesIterator()=0 | bpp::AssociationTreeGraphImplObserver< class, class, class > | pure virtual |
| allEdgesIterator() | bpp::AssociationTreeGraphImplObserver< class, class, class > | virtual |
| allEdgesIterator() const | bpp::AssociationTreeGraphImplObserver< class, class, class > | |
| allNodesIterator()=0 | bpp::AssociationTreeGraphImplObserver< class, class, class > | pure virtual |
| allNodesIterator() const=0 | bpp::AssociationTreeGraphImplObserver< class, class, class > | pure virtual |
| allNodesIterator() | bpp::AssociationTreeGraphImplObserver< class, class, class > | virtual |
| allNodesIterator() const | bpp::AssociationTreeGraphImplObserver< class, class, class > | virtual |
| allNodesIterator()=0 | bpp::AssociationTreeGraphImplObserver< class, class, class > | pure virtual |
| allNodesIterator() const=0 | bpp::AssociationTreeGraphImplObserver< class, class, class > | pure virtual |
| allNodesIterator() | bpp::AssociationTreeGraphImplObserver< class, class, class > | virtual |
| allNodesIterator() const | bpp::AssociationTreeGraphImplObserver< class, class, class > | virtual |
| associateEdge(std::shared_ptr< E > edgeObject, EdgeGraphid edge)=0 | bpp::AssociationTreeGraphImplObserver< class, class, class > | pure virtual |
| associateEdge(Eref edgeObject, EdgeGraphid graphEdge) | bpp::AssociationTreeGraphImplObserver< class, class, class > | virtual |
| associateEdge(std::shared_ptr< E > edgeObject, EdgeGraphid edge)=0 | bpp::AssociationTreeGraphImplObserver< class, class, class > | pure virtual |
| associateEdge(Eref edgeObject, EdgeGraphid graphEdge) | bpp::AssociationTreeGraphImplObserver< class, class, class > | virtual |
| AssociationGraphImplObserver< N, E, TreeGraphImpl >::associateEdge(Eref edgeObject, EdgeGraphid graphEdge) | AssociationGraphImplObserver< N, E, TreeGraphImpl > | |
| associateNode(std::shared_ptr< N > nodeObject, NodeGraphid node)=0 | bpp::AssociationTreeGraphImplObserver< class, class, class > | pure virtual |
| associateNode(Nref nodeObject, NodeGraphid graphNode) | bpp::AssociationTreeGraphImplObserver< class, class, class > | virtual |
| associateNode(std::shared_ptr< N > nodeObject, NodeGraphid node)=0 | bpp::AssociationTreeGraphImplObserver< class, class, class > | pure virtual |
| associateNode(Nref nodeObject, NodeGraphid graphNode) | bpp::AssociationTreeGraphImplObserver< class, class, class > | virtual |
| AssociationGraphImplObserver< N, E, TreeGraphImpl >::associateNode(Nref nodeObject, NodeGraphid graphNode) | AssociationGraphImplObserver< N, E, TreeGraphImpl > | |
| AssociationGraphImplObserver(bool directed=false) | AssociationGraphImplObserver< N, E, TreeGraphImpl > | |
| AssociationGraphImplObserver(std::shared_ptr< TreeGraphImpl > subjectGraph=00) | AssociationGraphImplObserver< N, E, TreeGraphImpl > | |
| AssociationGraphImplObserver(AssociationGraphImplObserver< N2, E2, TreeGraphImpl > const &graphObserver) | AssociationGraphImplObserver< N, E, TreeGraphImpl > | |
| AssociationGraphImplObserver(AssociationGraphImplObserver< N, E, TreeGraphImpl > const &graphObserver) | AssociationGraphImplObserver< N, E, TreeGraphImpl > | |
| AssociationTreeGraphImplObserver(bool rooted=false) | bpp::AssociationTreeGraphImplObserver< class, class, class > | |
| AssociationTreeGraphImplObserver(std::shared_ptr< TreeGraphImpl > subjectTreeGraph) | bpp::AssociationTreeGraphImplObserver< class, class, class > | |
| AssociationTreeGraphImplObserver(bpp::AssociationTreeGraphImplObserver< N, E, TreeGraphImpl > const &treeGraphObserver) | bpp::AssociationTreeGraphImplObserver< class, class, class > | |
| AssociationTreeGraphImplObserver(bpp::AssociationTreeGraphImplObserver< N2, E2, TreeGraphImpl > const &treeGraphObserver) | bpp::AssociationTreeGraphImplObserver< class, class, class > | |
| BOTH | bpp::AssociationTreeGraphImplObserver< class, class, class > | private |
| BranchedModelSet() | bpp::BranchedModelSet | inline |
| branchesIterator(std::shared_ptr< N > node) | bpp::AssociationTreeGraphImplObserver< class, class, class > | virtual |
| branchesIterator(std::shared_ptr< N > node) const | bpp::AssociationTreeGraphImplObserver< class, class, class > | virtual |
| clone() const | bpp::SingleProcessSubstitutionMapping | inlinevirtual |
| computeCounts(short unresolvedOption=SubstitutionMappingTools::UNRESOLVED_ZERO, double threshold=-1, bool verbose=true) | bpp::SingleProcessSubstitutionMapping | inlinevirtual |
| computeNormalizations(const ParameterList &nullParams, short unresolvedOption=SubstitutionMappingTools::UNRESOLVED_ZERO, bool verbose=true) | bpp::SingleProcessSubstitutionMapping | virtual |
| copy(const A &a, typename std::enable_if< !std::is_base_of< B, A >::value &&!std::is_abstract< B >::value, B * >::type *=0) | bpp::AssociationTreeGraphImplObserver< class, class, class > | static |
| copy(const A &a, typename std::enable_if< !std::is_base_of< B, A >::value &&std::is_abstract< B >::value, B * >::type *=0) | bpp::AssociationTreeGraphImplObserver< class, class, class > | static |
| copy(const A &a, typename std::enable_if< std::is_base_of< B, A >::value &&!std::is_abstract< A >::value, B * >::type *=0) | bpp::AssociationTreeGraphImplObserver< class, class, class > | static |
| 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) | bpp::AssociationTreeGraphImplObserver< class, class, class > | static |
| 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) | bpp::AssociationTreeGraphImplObserver< class, class, class > | static |
| AssociationGraphImplObserver< N, E, TreeGraphImpl >::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) | AssociationGraphImplObserver< N, E, TreeGraphImpl > | static |
| AssociationGraphImplObserver< N, E, TreeGraphImpl >::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) | AssociationGraphImplObserver< N, E, TreeGraphImpl > | static |
| counts() override | bpp::AbstractSinglePhyloSubstitutionMapping | inlinevirtual |
| counts() const override | bpp::AbstractSinglePhyloSubstitutionMapping | inlinevirtual |
| counts_ | bpp::AbstractSinglePhyloSubstitutionMapping | protected |
| countsPerformed() const override | bpp::AbstractSinglePhyloSubstitutionMapping | inlinevirtual |
| createNode(std::shared_ptr< N > newNodeObject)=0 | bpp::AssociationTreeGraphImplObserver< class, class, class > | pure virtual |
| createNode(std::shared_ptr< N > objectOriginNode, std::shared_ptr< N > newNodeObject, std::shared_ptr< E > newEdgeObject=00)=0 | bpp::AssociationTreeGraphImplObserver< class, class, class > | pure virtual |
| createNode(Nref nodeObject) | bpp::AssociationTreeGraphImplObserver< class, class, class > | virtual |
| createNode(Nref objectOriginNode, Nref newNodeObject, Eref newEdgeObject=00) | bpp::AssociationTreeGraphImplObserver< class, class, class > | virtual |
| createNode(std::shared_ptr< N > newNodeObject)=0 | bpp::AssociationTreeGraphImplObserver< class, class, class > | pure virtual |
| createNode(std::shared_ptr< N > objectOriginNode, std::shared_ptr< N > newNodeObject, std::shared_ptr< E > newEdgeObject=00)=0 | bpp::AssociationTreeGraphImplObserver< class, class, class > | pure virtual |
| createNode(Nref nodeObject) | bpp::AssociationTreeGraphImplObserver< class, class, class > | virtual |
| createNode(Nref objectOriginNode, Nref newNodeObject, Eref newEdgeObject=00) | bpp::AssociationTreeGraphImplObserver< class, class, class > | virtual |
| deletedEdgesUpdate(const std::vector< unsigned int > &edgesToDelete)=0 | bpp::AssociationTreeGraphImplObserver< class, class, class > | pure virtual |
| deletedEdgesUpdate(const std::vector< unsigned int > &edgesToDelete) | bpp::AssociationTreeGraphImplObserver< class, class, class > | virtual |
| deletedEdgesUpdate(const std::vector< unsigned int > &edgesToDelete)=0 | bpp::AssociationTreeGraphImplObserver< class, class, class > | pure virtual |
| deletedEdgesUpdate(const std::vector< unsigned int > &edgesToDelete) | bpp::AssociationTreeGraphImplObserver< class, class, class > | virtual |
| deletedNodesUpdate(const std::vector< unsigned int > &nodesToDelete)=0 | bpp::AssociationTreeGraphImplObserver< class, class, class > | pure virtual |
| deletedNodesUpdate(const std::vector< unsigned int > &nodesToDelete) | bpp::AssociationTreeGraphImplObserver< class, class, class > | virtual |
| deletedNodesUpdate(const std::vector< unsigned int > &nodesToDelete)=0 | bpp::AssociationTreeGraphImplObserver< class, class, class > | pure virtual |
| deletedNodesUpdate(const std::vector< unsigned int > &nodesToDelete) | bpp::AssociationTreeGraphImplObserver< class, class, class > | virtual |
| deleteNode(std::shared_ptr< N > nodeObject)=0 | bpp::AssociationTreeGraphImplObserver< class, class, class > | pure virtual |
| deleteNode(Nref nodeObject) | bpp::AssociationTreeGraphImplObserver< class, class, class > | virtual |
| deleteNode(std::shared_ptr< N > nodeObject)=0 | bpp::AssociationTreeGraphImplObserver< class, class, class > | pure virtual |
| deleteNode(Nref nodeObject) | bpp::AssociationTreeGraphImplObserver< class, class, class > | virtual |
| dissociateEdge(std::shared_ptr< E > edgeObject)=0 | bpp::AssociationTreeGraphImplObserver< class, class, class > | pure virtual |
| dissociateEdge(Eref edgeObject) | bpp::AssociationTreeGraphImplObserver< class, class, class > | virtual |
| dissociateEdge(std::shared_ptr< E > edgeObject)=0 | bpp::AssociationTreeGraphImplObserver< class, class, class > | pure virtual |
| dissociateEdge(Eref edgeObject) | bpp::AssociationTreeGraphImplObserver< class, class, class > | virtual |
| dissociateNode(std::shared_ptr< N > nodeObject)=0 | bpp::AssociationTreeGraphImplObserver< class, class, class > | pure virtual |
| dissociateNode(Nref nodeObject) | bpp::AssociationTreeGraphImplObserver< class, class, class > | virtual |
| dissociateNode(std::shared_ptr< N > nodeObject)=0 | bpp::AssociationTreeGraphImplObserver< class, class, class > | pure virtual |
| dissociateNode(Nref nodeObject) | bpp::AssociationTreeGraphImplObserver< class, class, class > | virtual |
| distances_ | bpp::AbstractSinglePhyloSubstitutionMapping | private |
| EdgeGraphid typedef | bpp::AssociationTreeGraphImplObserver< class, class, class > | |
| EdgeIndex typedef | bpp::AssociationTreeGraphImplObserver< class, class, class > | |
| EdgeIterator typedef | bpp::AssociationTreeGraphImplObserver< class, class, class > | |
| edgeToString(const Eref edgeObject) const | bpp::AssociationTreeGraphImplObserver< class, class, class > | |
| Eref typedef | bpp::AssociationTreeGraphImplObserver< class, class, class > | |
| EToGraphid_ | bpp::AssociationTreeGraphImplObserver< class, class, class > | private |
| EToIndex_ | bpp::AssociationTreeGraphImplObserver< class, class, class > | private |
| factors_ | bpp::AbstractSinglePhyloSubstitutionMapping | protected |
| getAllEdges() const=0 | bpp::AssociationTreeGraphImplObserver< class, class, class > | pure virtual |
| getAllEdges() const | bpp::AssociationTreeGraphImplObserver< class, class, class > | virtual |
| getAllEdges() const=0 | bpp::AssociationTreeGraphImplObserver< class, class, class > | pure virtual |
| getAllEdges() const | bpp::AssociationTreeGraphImplObserver< class, class, class > | virtual |
| getAllEdgesIndexes() const=0 | bpp::AssociationTreeGraphImplObserver< class, class, class > | pure virtual |
| getAllEdgesIndexes() const | bpp::AssociationTreeGraphImplObserver< class, class, class > | virtual |
| getAllEdgesIndexes() const=0 | bpp::AssociationTreeGraphImplObserver< class, class, class > | pure virtual |
| getAllEdgesIndexes() const | bpp::AssociationTreeGraphImplObserver< class, class, class > | virtual |
| getAllInnerNodes() const=0 | bpp::AssociationTreeGraphImplObserver< class, class, class > | pure virtual |
| getAllInnerNodes() const | bpp::AssociationTreeGraphImplObserver< class, class, class > | virtual |
| getAllInnerNodes() const=0 | bpp::AssociationTreeGraphImplObserver< class, class, class > | pure virtual |
| getAllInnerNodes() const | bpp::AssociationTreeGraphImplObserver< class, class, class > | virtual |
| getAllInnerNodesIndexes() const=0 | bpp::AssociationTreeGraphImplObserver< class, class, class > | pure virtual |
| getAllInnerNodesIndexes() const | bpp::AssociationTreeGraphImplObserver< class, class, class > | virtual |
| getAllInnerNodesIndexes() const=0 | bpp::AssociationTreeGraphImplObserver< class, class, class > | pure virtual |
| getAllInnerNodesIndexes() const | bpp::AssociationTreeGraphImplObserver< class, class, class > | virtual |
| getAllLeaves() const=0 | bpp::AssociationTreeGraphImplObserver< class, class, class > | pure virtual |
| getAllLeaves() const | bpp::AssociationTreeGraphImplObserver< class, class, class > | virtual |
| getAllLeaves() const=0 | bpp::AssociationTreeGraphImplObserver< class, class, class > | pure virtual |
| getAllLeaves() const | bpp::AssociationTreeGraphImplObserver< class, class, class > | virtual |
| getAllLeavesIndexes() const=0 | bpp::AssociationTreeGraphImplObserver< class, class, class > | pure virtual |
| getAllLeavesIndexes() const | bpp::AssociationTreeGraphImplObserver< class, class, class > | virtual |
| getAllLeavesIndexes() const=0 | bpp::AssociationTreeGraphImplObserver< class, class, class > | pure virtual |
| getAllLeavesIndexes() const | bpp::AssociationTreeGraphImplObserver< class, class, class > | virtual |
| getAllNodes() const=0 | bpp::AssociationTreeGraphImplObserver< class, class, class > | pure virtual |
| getAllNodes() const | bpp::AssociationTreeGraphImplObserver< class, class, class > | virtual |
| getAllNodes() const=0 | bpp::AssociationTreeGraphImplObserver< class, class, class > | pure virtual |
| getAllNodes() const | bpp::AssociationTreeGraphImplObserver< class, class, class > | virtual |
| getAllNodesIndexes() const=0 | bpp::AssociationTreeGraphImplObserver< class, class, class > | pure virtual |
| getAllNodesIndexes() const | bpp::AssociationTreeGraphImplObserver< class, class, class > | virtual |
| getAllNodesIndexes() const=0 | bpp::AssociationTreeGraphImplObserver< class, class, class > | pure virtual |
| getAllNodesIndexes() const | bpp::AssociationTreeGraphImplObserver< class, class, class > | virtual |
| getBranches(const std::shared_ptr< N > node) const | bpp::AssociationTreeGraphImplObserver< class, class, class > | virtual |
| getBranches(const NodeIndex node) const | bpp::AssociationTreeGraphImplObserver< class, class, class > | virtual |
| getBranchesWithModel(size_t index) const override | bpp::AbstractSinglePhyloSubstitutionMapping | inlinevirtual |
| getDegree(const Nref node) const | bpp::AssociationTreeGraphImplObserver< class, class, class > | |
| getDegree(const Nref node) const | bpp::AssociationTreeGraphImplObserver< class, class, class > | |
| getDistances() const | bpp::AbstractSinglePhyloSubstitutionMapping | inline |
| getEdge(EdgeIndex edgeIndex) const=0 | bpp::AssociationTreeGraphImplObserver< class, class, class > | pure virtual |
| getEdge(EdgeIndex edge) const | bpp::AssociationTreeGraphImplObserver< class, class, class > | virtual |
| getEdge(EdgeIndex edgeIndex) const=0 | bpp::AssociationTreeGraphImplObserver< class, class, class > | pure virtual |
| getEdge(EdgeIndex edge) const | bpp::AssociationTreeGraphImplObserver< class, class, class > | virtual |
| AssociationGraphImplObserver< N, E, TreeGraphImpl >::getEdge(EdgeIndex edge) const | AssociationGraphImplObserver< N, E, TreeGraphImpl > | |
| getEdgeFromGraphid(EdgeGraphid)=0 | bpp::AssociationTreeGraphImplObserver< class, class, class > | pure virtual |
| getEdgeFromGraphid(EdgeGraphid) const=0 | bpp::AssociationTreeGraphImplObserver< class, class, class > | pure virtual |
| getEdgeFromGraphid(EdgeGraphid edge) | bpp::AssociationTreeGraphImplObserver< class, class, class > | virtual |
| getEdgeFromGraphid(EdgeGraphid edge) const | bpp::AssociationTreeGraphImplObserver< class, class, class > | virtual |
| getEdgeFromGraphid(EdgeGraphid)=0 | bpp::AssociationTreeGraphImplObserver< class, class, class > | pure virtual |
| getEdgeFromGraphid(EdgeGraphid) const=0 | bpp::AssociationTreeGraphImplObserver< class, class, class > | pure virtual |
| getEdgeFromGraphid(EdgeGraphid edge) | bpp::AssociationTreeGraphImplObserver< class, class, class > | virtual |
| getEdgeFromGraphid(EdgeGraphid edge) const | bpp::AssociationTreeGraphImplObserver< class, class, class > | virtual |
| AssociationGraphImplObserver< N, E, TreeGraphImpl >::getEdgeFromGraphid(EdgeGraphid edge) | AssociationGraphImplObserver< N, E, TreeGraphImpl > | |
| AssociationGraphImplObserver< N, E, TreeGraphImpl >::getEdgeFromGraphid(EdgeGraphid edge) const | AssociationGraphImplObserver< N, E, TreeGraphImpl > | |
| getEdgeGraphid(const std::shared_ptr< E > edgeObject) const=0 | bpp::AssociationTreeGraphImplObserver< class, class, class > | pure virtual |
| getEdgeGraphid(const Eref edgeObject) const | bpp::AssociationTreeGraphImplObserver< class, class, class > | virtual |
| getEdgeGraphid(const std::shared_ptr< E > edgeObject) const=0 | bpp::AssociationTreeGraphImplObserver< class, class, class > | pure virtual |
| getEdgeGraphid(const Eref edgeObject) const | bpp::AssociationTreeGraphImplObserver< class, class, class > | virtual |
| getEdgeIndex(const std::shared_ptr< E > edgeObject) const=0 | bpp::AssociationTreeGraphImplObserver< class, class, class > | pure virtual |
| getEdgeIndex(const Eref edgeObject) const | bpp::AssociationTreeGraphImplObserver< class, class, class > | virtual |
| getEdgeIndex(const std::shared_ptr< E > edgeObject) const=0 | bpp::AssociationTreeGraphImplObserver< class, class, class > | pure virtual |
| getEdgeIndex(const Eref edgeObject) const | bpp::AssociationTreeGraphImplObserver< class, class, class > | virtual |
| getEdgeIndexes(std::vector< std::shared_ptr< E >> edgeObjects) const=0 | bpp::AssociationTreeGraphImplObserver< class, class, class > | pure virtual |
| getEdgeIndexes(std::vector< Eref > edges) const | bpp::AssociationTreeGraphImplObserver< class, class, class > | |
| getEdgeIndexes(std::vector< std::shared_ptr< E >> edgeObjects) const=0 | bpp::AssociationTreeGraphImplObserver< class, class, class > | pure virtual |
| getEdgeIndexes(std::vector< Eref > edges) const | bpp::AssociationTreeGraphImplObserver< class, class, class > | |
| getEdgeLinking(std::shared_ptr< N > nodeA, std::shared_ptr< N > nodeB) const=0 | bpp::AssociationTreeGraphImplObserver< class, class, class > | pure virtual |
| getEdgeLinking(Nref nodeA, Nref nodeB) const | bpp::AssociationTreeGraphImplObserver< class, class, class > | virtual |
| getEdgeLinking(std::shared_ptr< N > nodeA, std::shared_ptr< N > nodeB) const=0 | bpp::AssociationTreeGraphImplObserver< class, class, class > | pure virtual |
| getEdgeLinking(Nref nodeA, Nref nodeB) const | bpp::AssociationTreeGraphImplObserver< class, class, class > | virtual |
| getEdgePathBetweenTwoNodes(const std::shared_ptr< N > nodeA, const std::shared_ptr< N > nodeB) const | bpp::AssociationTreeGraphImplObserver< class, class, class > | virtual |
| getEdgePathBetweenTwoNodes(const NodeIndex nodeA, const NodeIndex nodeB, bool includeAncestor=true) const | bpp::AssociationTreeGraphImplObserver< class, class, class > | |
| getEdges(const std::shared_ptr< N > node) const=0 | bpp::AssociationTreeGraphImplObserver< class, class, class > | pure virtual |
| getEdges(NodeIndex node) const=0 | bpp::AssociationTreeGraphImplObserver< class, class, class > | pure virtual |
| getEdges(const Nref node) const | bpp::AssociationTreeGraphImplObserver< class, class, class > | virtual |
| getEdges(NodeIndex node) const | bpp::AssociationTreeGraphImplObserver< class, class, class > | virtual |
| getEdges(const std::shared_ptr< N > node) const=0 | bpp::AssociationTreeGraphImplObserver< class, class, class > | pure virtual |
| getEdges(NodeIndex node) const=0 | bpp::AssociationTreeGraphImplObserver< class, class, class > | pure virtual |
| getEdges(const Nref node) const | bpp::AssociationTreeGraphImplObserver< class, class, class > | virtual |
| getEdges(NodeIndex node) const | bpp::AssociationTreeGraphImplObserver< class, class, class > | virtual |
| AssociationGraphImplObserver< N, E, TreeGraphImpl >::getEdges(NodeIndex node) const | AssociationGraphImplObserver< N, E, TreeGraphImpl > | |
| getEdges_(const Nref nodeObject, neighborType type) const | bpp::AssociationTreeGraphImplObserver< class, class, class > | private |
| getEdgesFromGraphid(std::vector< EdgeGraphid >) const=0 | bpp::AssociationTreeGraphImplObserver< class, class, class > | pure virtual |
| getEdgesFromGraphid(std::vector< EdgeGraphid > edges) const | bpp::AssociationTreeGraphImplObserver< class, class, class > | virtual |
| getEdgesFromGraphid(std::vector< EdgeGraphid >) const=0 | bpp::AssociationTreeGraphImplObserver< class, class, class > | pure virtual |
| getEdgesFromGraphid(std::vector< EdgeGraphid > edges) const | bpp::AssociationTreeGraphImplObserver< class, class, class > | virtual |
| AssociationGraphImplObserver< N, E, TreeGraphImpl >::getEdgesFromGraphid(std::vector< EdgeGraphid > edges) const | AssociationGraphImplObserver< N, E, TreeGraphImpl > | |
| getEdgeToFather(const std::shared_ptr< N > nodeObject) const | bpp::AssociationTreeGraphImplObserver< class, class, class > | virtual |
| getEdgeToFather(const NodeIndex index) const | bpp::AssociationTreeGraphImplObserver< class, class, class > | virtual |
| getFatherOfEdge(const std::shared_ptr< E > edge) const | bpp::AssociationTreeGraphImplObserver< class, class, class > | virtual |
| getFatherOfEdge(const EdgeIndex edge) const | bpp::AssociationTreeGraphImplObserver< class, class, class > | virtual |
| getFatherOfNode(const std::shared_ptr< N > nodeObject) const | bpp::AssociationTreeGraphImplObserver< class, class, class > | virtual |
| getGraph() const | bpp::AssociationTreeGraphImplObserver< class, class, class > | |
| getGraph() | bpp::AssociationTreeGraphImplObserver< class, class, class > | |
| getIncomingEdges(const std::shared_ptr< N > node) const=0 | bpp::AssociationTreeGraphImplObserver< class, class, class > | pure virtual |
| getIncomingEdges(NodeIndex node) const=0 | bpp::AssociationTreeGraphImplObserver< class, class, class > | pure virtual |
| getIncomingEdges(const Nref node) const | bpp::AssociationTreeGraphImplObserver< class, class, class > | virtual |
| getIncomingEdges(NodeIndex node) const | bpp::AssociationTreeGraphImplObserver< class, class, class > | virtual |
| getIncomingEdges(const std::shared_ptr< N > node) const=0 | bpp::AssociationTreeGraphImplObserver< class, class, class > | pure virtual |
| getIncomingEdges(NodeIndex node) const=0 | bpp::AssociationTreeGraphImplObserver< class, class, class > | pure virtual |
| getIncomingEdges(const Nref node) const | bpp::AssociationTreeGraphImplObserver< class, class, class > | virtual |
| getIncomingEdges(NodeIndex node) const | bpp::AssociationTreeGraphImplObserver< class, class, class > | virtual |
| AssociationGraphImplObserver< N, E, TreeGraphImpl >::getIncomingEdges(NodeIndex node) const | AssociationGraphImplObserver< N, E, TreeGraphImpl > | |
| getIncomingNeighbors(const std::shared_ptr< N > node) const=0 | bpp::AssociationTreeGraphImplObserver< class, class, class > | pure virtual |
| getIncomingNeighbors(NodeIndex node) const=0 | bpp::AssociationTreeGraphImplObserver< class, class, class > | pure virtual |
| getIncomingNeighbors(const Nref node) const | bpp::AssociationTreeGraphImplObserver< class, class, class > | virtual |
| getIncomingNeighbors(NodeIndex node) const | bpp::AssociationTreeGraphImplObserver< class, class, class > | virtual |
| getIncomingNeighbors(const std::shared_ptr< N > node) const=0 | bpp::AssociationTreeGraphImplObserver< class, class, class > | pure virtual |
| getIncomingNeighbors(NodeIndex node) const=0 | bpp::AssociationTreeGraphImplObserver< class, class, class > | pure virtual |
| getIncomingNeighbors(const Nref node) const | bpp::AssociationTreeGraphImplObserver< class, class, class > | virtual |
| getIncomingNeighbors(NodeIndex node) const | bpp::AssociationTreeGraphImplObserver< class, class, class > | virtual |
| AssociationGraphImplObserver< N, E, TreeGraphImpl >::getIncomingNeighbors(NodeIndex node) const | AssociationGraphImplObserver< N, E, TreeGraphImpl > | |
| getLeavesFromNode(std::shared_ptr< N > node, unsigned int maxDepth) const=0 | bpp::AssociationTreeGraphImplObserver< class, class, class > | pure virtual |
| getLeavesFromNode(Nref node, unsigned int maxDepth) const | bpp::AssociationTreeGraphImplObserver< class, class, class > | virtual |
| getLeavesFromNode(std::shared_ptr< N > node, unsigned int maxDepth) const=0 | bpp::AssociationTreeGraphImplObserver< class, class, class > | pure virtual |
| getLeavesFromNode(Nref node, unsigned int maxDepth) const | bpp::AssociationTreeGraphImplObserver< class, class, class > | virtual |
| getLeavesUnderNode(std::shared_ptr< N > node) const | bpp::AssociationTreeGraphImplObserver< class, class, class > | virtual |
| getLeavesUnderNode(NodeIndex node) const | bpp::AssociationTreeGraphImplObserver< class, class, class > | |
| getLikelihoodCalculationSingleProcess() | bpp::SingleProcessSubstitutionMapping | inline |
| getLikelihoodCalculationSingleProcess() const | bpp::SingleProcessSubstitutionMapping | inline |
| getModel(unsigned int branchId, size_t classIndex) const override | bpp::AbstractSinglePhyloSubstitutionMapping | inlinevirtual |
| getModel(size_t index) | bpp::AbstractSinglePhyloSubstitutionMapping | inline |
| getModel(size_t index) const override | bpp::AbstractSinglePhyloSubstitutionMapping | inlinevirtual |
| getModelForBranch(uint branchId) override | bpp::AbstractSinglePhyloSubstitutionMapping | inline |
| getModelForBranch(uint branchId) const override | bpp::AbstractSinglePhyloSubstitutionMapping | inline |
| bpp::BranchedModelSet::getModelForBranch(unsigned int branchId) const =0 | bpp::BranchedModelSet | pure virtual |
| bpp::BranchedModelSet::getModelForBranch(unsigned int branchId)=0 | bpp::BranchedModelSet | pure virtual |
| getModelNumbers() const | bpp::SingleProcessSubstitutionMapping | inlinevirtual |
| getNeighbors(const std::shared_ptr< N > node) const=0 | bpp::AssociationTreeGraphImplObserver< class, class, class > | pure virtual |
| getNeighbors(NodeIndex node) const=0 | bpp::AssociationTreeGraphImplObserver< class, class, class > | pure virtual |
| getNeighbors(const Nref node) const | bpp::AssociationTreeGraphImplObserver< class, class, class > | virtual |
| getNeighbors(NodeIndex node) const | bpp::AssociationTreeGraphImplObserver< class, class, class > | virtual |
| getNeighbors(const std::shared_ptr< N > node) const=0 | bpp::AssociationTreeGraphImplObserver< class, class, class > | pure virtual |
| getNeighbors(NodeIndex node) const=0 | bpp::AssociationTreeGraphImplObserver< class, class, class > | pure virtual |
| getNeighbors(const Nref node) const | bpp::AssociationTreeGraphImplObserver< class, class, class > | virtual |
| getNeighbors(NodeIndex node) const | bpp::AssociationTreeGraphImplObserver< class, class, class > | virtual |
| AssociationGraphImplObserver< N, E, TreeGraphImpl >::getNeighbors(NodeIndex node) const | AssociationGraphImplObserver< N, E, TreeGraphImpl > | |
| getNeighbors_(const Nref nodeObject, neighborType type) const | bpp::AssociationTreeGraphImplObserver< class, class, class > | private |
| getNode(NodeIndex nodeIndex) const=0 | bpp::AssociationTreeGraphImplObserver< class, class, class > | pure virtual |
| getNode(NodeIndex node) const | bpp::AssociationTreeGraphImplObserver< class, class, class > | virtual |
| getNode(NodeIndex nodeIndex) const=0 | bpp::AssociationTreeGraphImplObserver< class, class, class > | pure virtual |
| getNode(NodeIndex node) const | bpp::AssociationTreeGraphImplObserver< class, class, class > | virtual |
| AssociationGraphImplObserver< N, E, TreeGraphImpl >::getNode(NodeIndex node) const | AssociationGraphImplObserver< N, E, TreeGraphImpl > | |
| getNodeFromGraphid(NodeGraphid) const=0 | bpp::AssociationTreeGraphImplObserver< class, class, class > | pure virtual |
| getNodeFromGraphid(NodeGraphid)=0 | bpp::AssociationTreeGraphImplObserver< class, class, class > | pure virtual |
| getNodeFromGraphid(NodeGraphid node) | bpp::AssociationTreeGraphImplObserver< class, class, class > | virtual |
| getNodeFromGraphid(NodeGraphid node) const | bpp::AssociationTreeGraphImplObserver< class, class, class > | virtual |
| getNodeFromGraphid(NodeGraphid) const=0 | bpp::AssociationTreeGraphImplObserver< class, class, class > | pure virtual |
| getNodeFromGraphid(NodeGraphid)=0 | bpp::AssociationTreeGraphImplObserver< class, class, class > | pure virtual |
| getNodeFromGraphid(NodeGraphid node) | bpp::AssociationTreeGraphImplObserver< class, class, class > | virtual |
| getNodeFromGraphid(NodeGraphid node) const | bpp::AssociationTreeGraphImplObserver< class, class, class > | virtual |
| AssociationGraphImplObserver< N, E, TreeGraphImpl >::getNodeFromGraphid(NodeGraphid node) | AssociationGraphImplObserver< N, E, TreeGraphImpl > | |
| AssociationGraphImplObserver< N, E, TreeGraphImpl >::getNodeFromGraphid(NodeGraphid node) const | AssociationGraphImplObserver< N, E, TreeGraphImpl > | |
| getNodeGraphid(const std::shared_ptr< N > nodeObject) const=0 | bpp::AssociationTreeGraphImplObserver< class, class, class > | pure virtual |
| getNodeGraphid(const Nref nodeObject) const | bpp::AssociationTreeGraphImplObserver< class, class, class > | virtual |
| getNodeGraphid(const std::shared_ptr< N > nodeObject) const=0 | bpp::AssociationTreeGraphImplObserver< class, class, class > | pure virtual |
| getNodeGraphid(const Nref nodeObject) const | bpp::AssociationTreeGraphImplObserver< class, class, class > | virtual |
| getNodeIndex(const std::shared_ptr< N > nodeObject) const=0 | bpp::AssociationTreeGraphImplObserver< class, class, class > | pure virtual |
| getNodeIndex(const Nref nodeObject) const | bpp::AssociationTreeGraphImplObserver< class, class, class > | virtual |
| getNodeIndex(const std::shared_ptr< N > nodeObject) const=0 | bpp::AssociationTreeGraphImplObserver< class, class, class > | pure virtual |
| getNodeIndex(const Nref nodeObject) const | bpp::AssociationTreeGraphImplObserver< class, class, class > | virtual |
| getNodeIndexes(std::vector< std::shared_ptr< N >> nodeObjects) const=0 | bpp::AssociationTreeGraphImplObserver< class, class, class > | pure virtual |
| getNodeIndexes(std::vector< Nref > nodes) const | bpp::AssociationTreeGraphImplObserver< class, class, class > | |
| getNodeIndexes(std::vector< std::shared_ptr< N >> nodeObjects) const=0 | bpp::AssociationTreeGraphImplObserver< class, class, class > | pure virtual |
| getNodeIndexes(std::vector< Nref > nodes) const | bpp::AssociationTreeGraphImplObserver< class, class, class > | |
| getNodePathBetweenTwoNodes(const std::shared_ptr< N > nodeA, const std::shared_ptr< N > nodeB, bool includeAncestor=true) const | bpp::AssociationTreeGraphImplObserver< class, class, class > | virtual |
| getNodePathBetweenTwoNodes(const NodeIndex nodeA, const NodeIndex nodeB, bool includeAncestor=true) const | bpp::AssociationTreeGraphImplObserver< class, class, class > | |
| getNodes(Eref edge) const | bpp::AssociationTreeGraphImplObserver< class, class, class > | |
| getNodes(Eref edge) const | bpp::AssociationTreeGraphImplObserver< class, class, class > | |
| getNodesFromGraphid(std::vector< NodeGraphid >) const=0 | bpp::AssociationTreeGraphImplObserver< class, class, class > | pure virtual |
| getNodesFromGraphid(std::vector< NodeGraphid > nodes) const | bpp::AssociationTreeGraphImplObserver< class, class, class > | virtual |
| getNodesFromGraphid(std::vector< NodeGraphid >) const=0 | bpp::AssociationTreeGraphImplObserver< class, class, class > | pure virtual |
| getNodesFromGraphid(std::vector< NodeGraphid > nodes) const | bpp::AssociationTreeGraphImplObserver< class, class, class > | virtual |
| AssociationGraphImplObserver< N, E, TreeGraphImpl >::getNodesFromGraphid(std::vector< NodeGraphid > nodes) const | AssociationGraphImplObserver< N, E, TreeGraphImpl > | |
| getNumberOfEdges() const | bpp::AssociationTreeGraphImplObserver< class, class, class > | |
| getNumberOfEdges() const | bpp::AssociationTreeGraphImplObserver< class, class, class > | |
| getNumberOfLeaves() const | bpp::AssociationTreeGraphImplObserver< class, class, class > | |
| getNumberOfLeaves() const | bpp::AssociationTreeGraphImplObserver< class, class, class > | |
| getNumberOfModels() const | bpp::SingleProcessSubstitutionMapping | inlinevirtual |
| getNumberOfNodes() const | bpp::AssociationTreeGraphImplObserver< class, class, class > | |
| getNumberOfNodes() const | bpp::AssociationTreeGraphImplObserver< class, class, class > | |
| getNumberOfSons(const std::shared_ptr< N > node) const | bpp::AssociationTreeGraphImplObserver< class, class, class > | virtual |
| getOutgoingEdges(const std::shared_ptr< N > node) const=0 | bpp::AssociationTreeGraphImplObserver< class, class, class > | pure virtual |
| getOutgoingEdges(NodeIndex node) const=0 | bpp::AssociationTreeGraphImplObserver< class, class, class > | pure virtual |
| getOutgoingEdges(const Nref node) const | bpp::AssociationTreeGraphImplObserver< class, class, class > | virtual |
| getOutgoingEdges(NodeIndex node) const | bpp::AssociationTreeGraphImplObserver< class, class, class > | virtual |
| getOutgoingEdges(const std::shared_ptr< N > node) const=0 | bpp::AssociationTreeGraphImplObserver< class, class, class > | pure virtual |
| getOutgoingEdges(NodeIndex node) const=0 | bpp::AssociationTreeGraphImplObserver< class, class, class > | pure virtual |
| getOutgoingEdges(const Nref node) const | bpp::AssociationTreeGraphImplObserver< class, class, class > | virtual |
| getOutgoingEdges(NodeIndex node) const | bpp::AssociationTreeGraphImplObserver< class, class, class > | virtual |
| AssociationGraphImplObserver< N, E, TreeGraphImpl >::getOutgoingEdges(NodeIndex node) const | AssociationGraphImplObserver< N, E, TreeGraphImpl > | |
| getOutgoingNeighbors(const std::shared_ptr< N > node) const=0 | bpp::AssociationTreeGraphImplObserver< class, class, class > | pure virtual |
| getOutgoingNeighbors(NodeIndex node) const=0 | bpp::AssociationTreeGraphImplObserver< class, class, class > | pure virtual |
| getOutgoingNeighbors(const Nref node) const | bpp::AssociationTreeGraphImplObserver< class, class, class > | virtual |
| getOutgoingNeighbors(NodeIndex node) const | bpp::AssociationTreeGraphImplObserver< class, class, class > | virtual |
| getOutgoingNeighbors(const std::shared_ptr< N > node) const=0 | bpp::AssociationTreeGraphImplObserver< class, class, class > | pure virtual |
| getOutgoingNeighbors(NodeIndex node) const=0 | bpp::AssociationTreeGraphImplObserver< class, class, class > | pure virtual |
| getOutgoingNeighbors(const Nref node) const | bpp::AssociationTreeGraphImplObserver< class, class, class > | virtual |
| getOutgoingNeighbors(NodeIndex node) const | bpp::AssociationTreeGraphImplObserver< class, class, class > | virtual |
| AssociationGraphImplObserver< N, E, TreeGraphImpl >::getOutgoingNeighbors(NodeIndex node) const | AssociationGraphImplObserver< N, E, TreeGraphImpl > | |
| getParameters() const override | bpp::AbstractSinglePhyloSubstitutionMapping | inlinevirtual |
| getRoot() const=0 | bpp::AssociationTreeGraphImplObserver< class, class, class > | pure virtual |
| getRoot() const | bpp::AssociationTreeGraphImplObserver< class, class, class > | virtual |
| getRoot() const=0 | bpp::AssociationTreeGraphImplObserver< class, class, class > | pure virtual |
| getRoot() const | bpp::AssociationTreeGraphImplObserver< class, class, class > | virtual |
| getRootIndex() const=0 | bpp::AssociationTreeGraphImplObserver< class, class, class > | pure virtual |
| getRootIndex() const | bpp::AssociationTreeGraphImplObserver< class, class, class > | virtual |
| getRootIndex() const=0 | bpp::AssociationTreeGraphImplObserver< class, class, class > | pure virtual |
| getRootIndex() const | bpp::AssociationTreeGraphImplObserver< class, class, class > | virtual |
| getSon(const std::shared_ptr< E > edge) const | bpp::AssociationTreeGraphImplObserver< class, class, class > | virtual |
| getSon(const EdgeIndex edge) const | bpp::AssociationTreeGraphImplObserver< class, class, class > | virtual |
| getSons(const std::shared_ptr< N > node) const | bpp::AssociationTreeGraphImplObserver< class, class, class > | virtual |
| getSons(const NodeIndex node) const | bpp::AssociationTreeGraphImplObserver< class, class, class > | virtual |
| getSubstitutionRegister() const | bpp::AbstractSinglePhyloSubstitutionMapping | inline |
| getSubtreeEdges(const std::shared_ptr< N > localRoot) const | bpp::AssociationTreeGraphImplObserver< class, class, class > | virtual |
| getSubtreeEdges(const NodeIndex localRoot) const | bpp::AssociationTreeGraphImplObserver< class, class, class > | |
| getSubtreeNodes(const std::shared_ptr< N > localRoot) const | bpp::AssociationTreeGraphImplObserver< class, class, class > | virtual |
| getSubtreeNodes(const NodeIndex localRoot) const | bpp::AssociationTreeGraphImplObserver< class, class, class > | |
| getWeights() const | bpp::AbstractSinglePhyloSubstitutionMapping | inline |
| graphidToE_ | bpp::AssociationTreeGraphImplObserver< class, class, class > | private |
| graphidToN_ | bpp::AssociationTreeGraphImplObserver< class, class, class > | private |
| hasEdge(EdgeIndex edgeIndex) const=0 | bpp::AssociationTreeGraphImplObserver< class, class, class > | pure virtual |
| hasEdge(EdgeIndex edge) const | bpp::AssociationTreeGraphImplObserver< class, class, class > | virtual |
| hasEdge(EdgeIndex edgeIndex) const=0 | bpp::AssociationTreeGraphImplObserver< class, class, class > | pure virtual |
| hasEdge(Eref edgeObject) const | bpp::AssociationTreeGraphImplObserver< class, class, class > | |
| hasEdge(EdgeIndex edge) const | bpp::AssociationTreeGraphImplObserver< class, class, class > | virtual |
| AssociationGraphImplObserver< N, E, TreeGraphImpl >::hasEdge(EdgeIndex edge) const | AssociationGraphImplObserver< N, E, TreeGraphImpl > | |
| hasEdgeIndex(const std::shared_ptr< E > edgeObject) const=0 | bpp::AssociationTreeGraphImplObserver< class, class, class > | pure virtual |
| hasEdgeIndex(const Eref edgeObject) const | bpp::AssociationTreeGraphImplObserver< class, class, class > | virtual |
| hasEdgeIndex(const std::shared_ptr< E > edgeObject) const=0 | bpp::AssociationTreeGraphImplObserver< class, class, class > | pure virtual |
| hasEdgeIndex(const Eref edgeObject) const | bpp::AssociationTreeGraphImplObserver< class, class, class > | virtual |
| hasFather(const std::shared_ptr< N > nodeObject) const | bpp::AssociationTreeGraphImplObserver< class, class, class > | virtual |
| hasFather(const NodeIndex index) const | bpp::AssociationTreeGraphImplObserver< class, class, class > | virtual |
| hasNode(NodeIndex nodeIndex) const=0 | bpp::AssociationTreeGraphImplObserver< class, class, class > | pure virtual |
| hasNode(NodeIndex node) const | bpp::AssociationTreeGraphImplObserver< class, class, class > | virtual |
| hasNode(NodeIndex nodeIndex) const=0 | bpp::AssociationTreeGraphImplObserver< class, class, class > | pure virtual |
| hasNode(Nref nodeObject) const | bpp::AssociationTreeGraphImplObserver< class, class, class > | |
| hasNode(NodeIndex node) const | bpp::AssociationTreeGraphImplObserver< class, class, class > | virtual |
| AssociationGraphImplObserver< N, E, TreeGraphImpl >::hasNode(NodeIndex node) const | AssociationGraphImplObserver< N, E, TreeGraphImpl > | |
| hasNodeIndex(const std::shared_ptr< N > nodeObject) const=0 | bpp::AssociationTreeGraphImplObserver< class, class, class > | pure virtual |
| hasNodeIndex(const Nref nodeObject) const | bpp::AssociationTreeGraphImplObserver< class, class, class > | virtual |
| hasNodeIndex(const std::shared_ptr< N > nodeObject) const=0 | bpp::AssociationTreeGraphImplObserver< class, class, class > | pure virtual |
| hasNodeIndex(const Nref nodeObject) const | bpp::AssociationTreeGraphImplObserver< class, class, class > | virtual |
| INCOMING | bpp::AssociationTreeGraphImplObserver< class, class, class > | private |
| incomingEdgesIterator(std::shared_ptr< N > node)=0 | bpp::AssociationTreeGraphImplObserver< class, class, class > | pure virtual |
| incomingEdgesIterator(Nref node) | bpp::AssociationTreeGraphImplObserver< class, class, class > | virtual |
| incomingEdgesIterator(Nref node) const | bpp::AssociationTreeGraphImplObserver< class, class, class > | |
| incomingEdgesIterator(std::shared_ptr< N > node)=0 | bpp::AssociationTreeGraphImplObserver< class, class, class > | pure virtual |
| incomingEdgesIterator(Nref node) | bpp::AssociationTreeGraphImplObserver< class, class, class > | virtual |
| incomingEdgesIterator(Nref node) const | bpp::AssociationTreeGraphImplObserver< class, class, class > | |
| incomingNeighborNodesIterator(std::shared_ptr< N > node)=0 | bpp::AssociationTreeGraphImplObserver< class, class, class > | pure virtual |
| incomingNeighborNodesIterator(std::shared_ptr< N > node) const=0 | bpp::AssociationTreeGraphImplObserver< class, class, class > | pure virtual |
| incomingNeighborNodesIterator(Nref node) | bpp::AssociationTreeGraphImplObserver< class, class, class > | virtual |
| incomingNeighborNodesIterator(Nref node) const | bpp::AssociationTreeGraphImplObserver< class, class, class > | virtual |
| incomingNeighborNodesIterator(std::shared_ptr< N > node)=0 | bpp::AssociationTreeGraphImplObserver< class, class, class > | pure virtual |
| incomingNeighborNodesIterator(std::shared_ptr< N > node) const=0 | bpp::AssociationTreeGraphImplObserver< class, class, class > | pure virtual |
| incomingNeighborNodesIterator(Nref node) | bpp::AssociationTreeGraphImplObserver< class, class, class > | virtual |
| incomingNeighborNodesIterator(Nref node) const | bpp::AssociationTreeGraphImplObserver< class, class, class > | virtual |
| indexToE_ | bpp::AssociationTreeGraphImplObserver< class, class, class > | private |
| indexToN_ | bpp::AssociationTreeGraphImplObserver< class, class, class > | private |
| isLeaf(const Nref node) const | bpp::AssociationTreeGraphImplObserver< class, class, class > | |
| isLeaf(const NodeIndex nodeid) const | bpp::AssociationTreeGraphImplObserver< class, class, class > | |
| isLeaf(const Nref node) const | bpp::AssociationTreeGraphImplObserver< class, class, class > | |
| isLeaf(const NodeIndex nodeid) const | bpp::AssociationTreeGraphImplObserver< class, class, class > | |
| AssociationGraphImplObserver< N, E, TreeGraphImpl >::isLeaf(const NodeIndex nodeid) const | AssociationGraphImplObserver< N, E, TreeGraphImpl > | |
| isRooted() const | bpp::AssociationTreeGraphImplObserver< class, class, class > | virtual |
| isValid() const | bpp::AssociationTreeGraphImplObserver< class, class, class > | virtual |
| link(std::shared_ptr< N > nodeObjectA, std::shared_ptr< N > nodeObjectB, std::shared_ptr< E > edgeObject=00)=0 | bpp::AssociationTreeGraphImplObserver< class, class, class > | pure virtual |
| link(Nref nodeObjectA, Nref nodeObjectB, Eref edgeObject=00) | bpp::AssociationTreeGraphImplObserver< class, class, class > | virtual |
| link(std::shared_ptr< N > nodeObjectA, std::shared_ptr< N > nodeObjectB, std::shared_ptr< E > edgeObject=00)=0 | bpp::AssociationTreeGraphImplObserver< class, class, class > | pure virtual |
| link(Nref nodeObjectA, Nref nodeObjectB, Eref edgeObject=00) | bpp::AssociationTreeGraphImplObserver< class, class, class > | virtual |
| matchParametersValues(const ParameterList &nullParams) override | bpp::AbstractSinglePhyloSubstitutionMapping | inlinevirtual |
| mModBrid_ | bpp::AbstractSinglePhyloSubstitutionMapping | private |
| modelColl_ | bpp::AbstractSinglePhyloSubstitutionMapping | private |
| modelTree typedef | bpp::AbstractSinglePhyloSubstitutionMapping | |
| MRCA(const std::vector< std::shared_ptr< N >> vNodeObject) const | bpp::AssociationTreeGraphImplObserver< class, class, class > | |
| neighborType enum name | bpp::AssociationTreeGraphImplObserver< class, class, class > | private |
| NodeGraphid typedef | bpp::AssociationTreeGraphImplObserver< class, class, class > | |
| NodeIndex typedef | bpp::AssociationTreeGraphImplObserver< class, class, class > | |
| NodeIterator typedef | bpp::AssociationTreeGraphImplObserver< class, class, class > | |
| nodeToString(const Nref nodeObject) const | bpp::AssociationTreeGraphImplObserver< class, class, class > | |
| normalizations() override | bpp::AbstractSinglePhyloSubstitutionMapping | inlinevirtual |
| normalizations() const override | bpp::AbstractSinglePhyloSubstitutionMapping | inlinevirtual |
| normalizationsPerformed() const override | bpp::AbstractSinglePhyloSubstitutionMapping | inlinevirtual |
| Nref typedef | bpp::AssociationTreeGraphImplObserver< class, class, class > | |
| NToGraphid_ | bpp::AssociationTreeGraphImplObserver< class, class, class > | private |
| NToIndex_ | bpp::AssociationTreeGraphImplObserver< class, class, class > | private |
| operator=(const SingleProcessSubstitutionMapping &sppm) | bpp::SingleProcessSubstitutionMapping | inline |
| bpp::AbstractSinglePhyloSubstitutionMapping::operator=(const AbstractSinglePhyloSubstitutionMapping &sppm) | bpp::AbstractSinglePhyloSubstitutionMapping | |
| bpp::AssociationTreeGraphImplObserver::operator=(bpp::AssociationTreeGraphImplObserver< N, E, TreeGraphImpl > const &treeGraphObserver) | bpp::AssociationTreeGraphImplObserver< class, class, class > | |
| AssociationGraphImplObserver< N, E, TreeGraphImpl >::operator=(bpp::AssociationGraphImplObserver< N, E, TreeGraphImpl > const &graphObserver) | AssociationGraphImplObserver< N, E, TreeGraphImpl > | |
| OUTGOING | bpp::AssociationTreeGraphImplObserver< class, class, class > | private |
| outgoingEdgesIterator(std::shared_ptr< N > node)=0 | bpp::AssociationTreeGraphImplObserver< class, class, class > | pure virtual |
| outgoingEdgesIterator(Nref node) | bpp::AssociationTreeGraphImplObserver< class, class, class > | virtual |
| outgoingEdgesIterator(Nref node) const | bpp::AssociationTreeGraphImplObserver< class, class, class > | |
| outgoingEdgesIterator(std::shared_ptr< N > node)=0 | bpp::AssociationTreeGraphImplObserver< class, class, class > | pure virtual |
| outgoingEdgesIterator(Nref node) | bpp::AssociationTreeGraphImplObserver< class, class, class > | virtual |
| outgoingEdgesIterator(Nref node) const | bpp::AssociationTreeGraphImplObserver< class, class, class > | |
| outgoingNeighborNodesIterator(std::shared_ptr< N > node)=0 | bpp::AssociationTreeGraphImplObserver< class, class, class > | pure virtual |
| outgoingNeighborNodesIterator(std::shared_ptr< N > node) const=0 | bpp::AssociationTreeGraphImplObserver< class, class, class > | pure virtual |
| outgoingNeighborNodesIterator(Nref node) | bpp::AssociationTreeGraphImplObserver< class, class, class > | virtual |
| outgoingNeighborNodesIterator(Nref node) const | bpp::AssociationTreeGraphImplObserver< class, class, class > | virtual |
| outgoingNeighborNodesIterator(std::shared_ptr< N > node)=0 | bpp::AssociationTreeGraphImplObserver< class, class, class > | pure virtual |
| outgoingNeighborNodesIterator(std::shared_ptr< N > node) const=0 | bpp::AssociationTreeGraphImplObserver< class, class, class > | pure virtual |
| outgoingNeighborNodesIterator(Nref node) | bpp::AssociationTreeGraphImplObserver< class, class, class > | virtual |
| outgoingNeighborNodesIterator(Nref node) const | bpp::AssociationTreeGraphImplObserver< class, class, class > | virtual |
| outputToDot(const std::string &fname, const std::string &name) const | bpp::AssociationTreeGraphImplObserver< class, class, class > | |
| outputToDot(std::ostream &out, const std::string &name) const | bpp::AssociationTreeGraphImplObserver< class, class, class > | |
| outputToDot(const std::string &fname, const std::string &name) const | bpp::AssociationTreeGraphImplObserver< class, class, class > | |
| outputToDot(std::ostream &out, const std::string &name) const | bpp::AssociationTreeGraphImplObserver< class, class, class > | |
| PhyloSubstitutionMapping() | bpp::PhyloSubstitutionMapping | inline |
| pReg_ | bpp::AbstractSinglePhyloSubstitutionMapping | private |
| pSPP_ | bpp::SingleProcessSubstitutionMapping | private |
| removeSon(const std::shared_ptr< N > node, const std::shared_ptr< N > son) | bpp::AssociationTreeGraphImplObserver< class, class, class > | virtual |
| removeSons(const std::shared_ptr< N > node) | bpp::AssociationTreeGraphImplObserver< class, class, class > | virtual |
| rootAt(const std::shared_ptr< N > root) | bpp::AssociationTreeGraphImplObserver< class, class, class > | virtual |
| setBranchedModelSet_() | bpp::SingleProcessSubstitutionMapping | private |
| setDistances(const AlphabetIndex2 &ndist) override | bpp::AbstractSinglePhyloSubstitutionMapping | inlinevirtual |
| setEdgeIndex(const std::shared_ptr< E > edgeObject, EdgeIndex index)=0 | bpp::AssociationTreeGraphImplObserver< class, class, class > | pure virtual |
| setEdgeIndex(const Eref edgeObject, EdgeIndex index) | bpp::AssociationTreeGraphImplObserver< class, class, class > | virtual |
| setEdgeIndex(const std::shared_ptr< E > edgeObject, EdgeIndex index)=0 | bpp::AssociationTreeGraphImplObserver< class, class, class > | pure virtual |
| setEdgeIndex(const Eref edgeObject, EdgeIndex index) | bpp::AssociationTreeGraphImplObserver< class, class, class > | virtual |
| AssociationGraphImplObserver< N, E, TreeGraphImpl >::setEdgeIndex(const Eref edgeObject, EdgeIndex index) | AssociationGraphImplObserver< N, E, TreeGraphImpl > | |
| setEdgeLinking(std::shared_ptr< N > nodeA, std::shared_ptr< N > nodeB, std::shared_ptr< E > edge)=0 | bpp::AssociationTreeGraphImplObserver< class, class, class > | pure virtual |
| setEdgeLinking(Nref nodeA, Nref nodeB, Eref edge) | bpp::AssociationTreeGraphImplObserver< class, class, class > | virtual |
| setEdgeLinking(std::shared_ptr< N > nodeA, std::shared_ptr< N > nodeB, std::shared_ptr< E > edge)=0 | bpp::AssociationTreeGraphImplObserver< class, class, class > | pure virtual |
| setEdgeLinking(Nref nodeA, Nref nodeB, Eref edge) | bpp::AssociationTreeGraphImplObserver< class, class, class > | virtual |
| setFather(const std::shared_ptr< N > nodeObject, const std::shared_ptr< N > fatherNodeObject, const std::shared_ptr< E > edgeObject=0) | bpp::AssociationTreeGraphImplObserver< class, class, class > | virtual |
| setNodeIndex(const std::shared_ptr< N > nodeObject, NodeIndex index)=0 | bpp::AssociationTreeGraphImplObserver< class, class, class > | pure virtual |
| setNodeIndex(const Nref nodeObject, NodeIndex index) | bpp::AssociationTreeGraphImplObserver< class, class, class > | virtual |
| setNodeIndex(const std::shared_ptr< N > nodeObject, NodeIndex index)=0 | bpp::AssociationTreeGraphImplObserver< class, class, class > | pure virtual |
| setNodeIndex(const Nref nodeObject, NodeIndex index) | bpp::AssociationTreeGraphImplObserver< class, class, class > | virtual |
| AssociationGraphImplObserver< N, E, TreeGraphImpl >::setNodeIndex(const Nref nodeObject, NodeIndex index) | AssociationGraphImplObserver< N, E, TreeGraphImpl > | |
| setRoot(const Nref newRoot) | bpp::AssociationTreeGraphImplObserver< class, class, class > | |
| setRoot(const Nref newRoot) | bpp::AssociationTreeGraphImplObserver< class, class, class > | |
| setSubstitutionRegister(std::shared_ptr< const SubstitutionRegisterInterface > reg) | bpp::AbstractSinglePhyloSubstitutionMapping | inline |
| SingleProcessSubstitutionMapping(std::shared_ptr< SingleProcessPhyloLikelihood > spp, std::shared_ptr< SubstitutionRegisterInterface > reg, std::shared_ptr< const AlphabetIndex2 > weights, std::shared_ptr< const AlphabetIndex2 > distances, double threshold=-1, bool verbose=true) | bpp::SingleProcessSubstitutionMapping | |
| SingleProcessSubstitutionMapping(const SingleProcessSubstitutionMapping &sppm) | bpp::SingleProcessSubstitutionMapping | inline |
| sonsIterator(std::shared_ptr< N > node) | bpp::AssociationTreeGraphImplObserver< class, class, class > | virtual |
| sonsIterator(std::shared_ptr< N > node) const | bpp::AssociationTreeGraphImplObserver< class, class, class > | virtual |
| subjectGraph_ | bpp::AssociationTreeGraphImplObserver< class, class, class > | protected |
| substitutionRegister() const | bpp::AbstractSinglePhyloSubstitutionMapping | inline |
| unlink(std::shared_ptr< N > nodeObjectA, std::shared_ptr< N > nodeObjectB)=0 | bpp::AssociationTreeGraphImplObserver< class, class, class > | pure virtual |
| unlink(Nref nodeObjectA, Nref nodeObjectB) | bpp::AssociationTreeGraphImplObserver< class, class, class > | virtual |
| unlink(std::shared_ptr< N > nodeObjectA, std::shared_ptr< N > nodeObjectB)=0 | bpp::AssociationTreeGraphImplObserver< class, class, class > | pure virtual |
| unlink(Nref nodeObjectA, Nref nodeObjectB) | bpp::AssociationTreeGraphImplObserver< class, class, class > | virtual |
| weights_ | bpp::AbstractSinglePhyloSubstitutionMapping | private |
| ~AbstractSinglePhyloSubstitutionMapping() | bpp::AbstractSinglePhyloSubstitutionMapping | inlinevirtual |
| ~AssociationGraphImplObserver() | AssociationGraphImplObserver< N, E, TreeGraphImpl > | |
| ~AssociationTreeGraphImplObserver() | bpp::AssociationTreeGraphImplObserver< class, class, class > | |
| ~BranchedModelSet() | bpp::BranchedModelSet | inlinevirtual |
| ~Clonable()=default | bpp::Clonable | virtual |
| ~PhyloSubstitutionMapping() | bpp::PhyloSubstitutionMapping | inlinevirtual |
| ~SingleProcessSubstitutionMapping() | bpp::SingleProcessSubstitutionMapping | inlinevirtual |
1.9.1