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bpp::ParametrizablePhyloTree Class Referenceabstract
PhyloTree with Parametrizable Phylo Branches. They SHARE their branch length parameters. More...
#include <Bpp/Phyl/Likelihood/ParametrizablePhyloTree.h>
Inheritance diagram for bpp::ParametrizablePhyloTree:
Collaboration diagram for bpp::ParametrizablePhyloTree:
Public Types | |
| typedef AssociationGraphObserver< N, E >::NodeIndex | NodeIndex |
| typedef AssociationGraphObserver< N, E >::EdgeIndex | EdgeIndex |
| typedef Graph::NodeId | NodeGraphid |
| typedef Graph::EdgeId | EdgeGraphid |
| typedef AssociationGraphObserver< N, E >::NodeIterator | NodeIterator |
| typedef AssociationGraphObserver< N, E >::EdgeIterator | EdgeIterator |
| typedef std::shared_ptr< E > | Eref |
| typedef std::shared_ptr< N > | Nref |
Public Member Functions | |
| ParametrizablePhyloTree (const PhyloTree &tree, const std::string &prefix="") | |
| ParametrizablePhyloTree (const ParametrizablePhyloTree &pTree) | |
| ParametrizablePhyloTree & | operator= (const ParametrizablePhyloTree &pTree) |
| ParametrizablePhyloTree * | clone () const |
| std::vector< std::string > | getAllLeavesNames () const |
| Vdouble | getBranchLengths () const |
| virtual void | setMinimumBranchLength (double minimum) |
| virtual void | setMaximumBranchLength (double maximum) |
| virtual double | getMinimumBranchLength () const |
| virtual double | getMaximumBranchLength () const |
| bool | isValid () const |
| std::shared_ptr< E > | getEdgeToFather (const std::shared_ptr< N > nodeObject) const |
| std::shared_ptr< E > | getEdgeToFather (const NodeIndex index) const |
| void | rootAt (const std::shared_ptr< N > root) |
| bool | isRooted () const |
| std::shared_ptr< N > | getFatherOfNode (const std::shared_ptr< N > nodeObject) const |
| bool | hasFather (const std::shared_ptr< N > nodeObject) const |
| bool | hasFather (const NodeIndex index) const |
| std::vector< std::shared_ptr< N > > | getSons (const std::shared_ptr< N > node) const |
| std::vector< NodeIndex > | getSons (const NodeIndex node) const |
| std::vector< std::shared_ptr< E > > | getBranches (const std::shared_ptr< N > node) const |
| std::vector< EdgeIndex > | getBranches (const NodeIndex node) const |
| std::shared_ptr< N > | getSon (const std::shared_ptr< E > edge) const |
| NodeIndex | getSon (const EdgeIndex edge) const |
| std::shared_ptr< N > | getFatherOfEdge (const std::shared_ptr< E > edge) const |
| NodeIndex | getFatherOfEdge (const EdgeIndex edge) const |
| size_t | getNumberOfSons (const std::shared_ptr< N > node) const |
| std::vector< std::shared_ptr< N > > | getLeavesUnderNode (std::shared_ptr< N > node) const |
| std::vector< NodeIndex > | getLeavesUnderNode (NodeIndex node) const |
| std::vector< std::shared_ptr< N > > | removeSons (const std::shared_ptr< N > node) |
| void | removeSon (const std::shared_ptr< N > node, const std::shared_ptr< N > son) |
| void | setFather (const std::shared_ptr< N > nodeObject, const std::shared_ptr< N > fatherNodeObject, const std::shared_ptr< E > edgeObject=0) |
| void | addSon (const std::shared_ptr< N > nodeObject, const std::shared_ptr< N > sonNodeObject, const std::shared_ptr< E > edgeObject=0) |
| std::unique_ptr< typename AssociationTreeGraphObserver< N, E >::NodeIterator > | sonsIterator (std::shared_ptr< N > node) |
| std::unique_ptr< typename AssociationTreeGraphObserver< N, E >::NodeIterator > | sonsIterator (std::shared_ptr< N > node) const |
| std::unique_ptr< typename AssociationTreeGraphObserver< N, E >::EdgeIterator > | branchesIterator (std::shared_ptr< N > node) |
| std::unique_ptr< typename AssociationTreeGraphObserver< N, E >::EdgeIterator > | branchesIterator (std::shared_ptr< N > node) const |
| std::vector< std::shared_ptr< N > > | getNodePathBetweenTwoNodes (const std::shared_ptr< N > nodeA, const std::shared_ptr< N > nodeB, bool includeAncestor=true) const |
| std::vector< NodeIndex > | getNodePathBetweenTwoNodes (const NodeIndex nodeA, const NodeIndex nodeB, bool includeAncestor=true) const |
| std::vector< std::shared_ptr< E > > | getEdgePathBetweenTwoNodes (const std::shared_ptr< N > nodeA, const std::shared_ptr< N > nodeB) const |
| std::vector< EdgeIndex > | getEdgePathBetweenTwoNodes (const NodeIndex nodeA, const NodeIndex nodeB, bool includeAncestor=true) const |
| std::vector< std::shared_ptr< N > > | getSubtreeNodes (const std::shared_ptr< N > localRoot) const |
| std::vector< NodeIndex > | getSubtreeNodes (const NodeIndex localRoot) const |
| std::vector< std::shared_ptr< E > > | getSubtreeEdges (const std::shared_ptr< N > localRoot) const |
| std::vector< EdgeIndex > | getSubtreeEdges (const NodeIndex localRoot) const |
| std::shared_ptr< N > | MRCA (const std::vector< std::shared_ptr< N > > vNodeObject) const |
| 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 |
| void | createNode (Nref nodeObject) |
| void | createNode (Nref objectOriginNode, Nref newNodeObject, Eref newEdgeObject=00) |
| 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 |
| void | createNode (Nref nodeObject) |
| void | createNode (Nref objectOriginNode, Nref newNodeObject, Eref newEdgeObject=00) |
| virtual void | link (std::shared_ptr< N > nodeObjectA, std::shared_ptr< N > nodeObjectB, std::shared_ptr< E > edgeObject=00)=0 |
| void | link (Nref nodeObjectA, Nref nodeObjectB, Eref edgeObject=00) |
| virtual void | link (std::shared_ptr< N > nodeObjectA, std::shared_ptr< N > nodeObjectB, std::shared_ptr< E > edgeObject=00)=0 |
| void | link (Nref nodeObjectA, Nref nodeObjectB, Eref edgeObject=00) |
| virtual void | unlink (std::shared_ptr< N > nodeObjectA, std::shared_ptr< N > nodeObjectB)=0 |
| void | unlink (Nref nodeObjectA, Nref nodeObjectB) |
| virtual void | unlink (std::shared_ptr< N > nodeObjectA, std::shared_ptr< N > nodeObjectB)=0 |
| void | unlink (Nref nodeObjectA, Nref nodeObjectB) |
| virtual void | deleteNode (std::shared_ptr< N > nodeObject)=0 |
| void | deleteNode (Nref nodeObject) |
| virtual void | deleteNode (std::shared_ptr< N > nodeObject)=0 |
| void | deleteNode (Nref nodeObject) |
| virtual void | associateNode (std::shared_ptr< N > nodeObject, NodeGraphid node)=0 |
| void | associateNode (Nref nodeObject, NodeGraphid graphNode) |
| virtual void | associateNode (std::shared_ptr< N > nodeObject, NodeGraphid node)=0 |
| void | associateNode (Nref nodeObject, NodeGraphid graphNode) |
| virtual void | associateEdge (std::shared_ptr< E > edgeObject, EdgeGraphid edge)=0 |
| void | associateEdge (Eref edgeObject, EdgeGraphid graphEdge) |
| virtual void | associateEdge (std::shared_ptr< E > edgeObject, EdgeGraphid edge)=0 |
| void | associateEdge (Eref edgeObject, EdgeGraphid graphEdge) |
| virtual void | dissociateNode (std::shared_ptr< N > nodeObject)=0 |
| void | dissociateNode (Nref nodeObject) |
| virtual void | dissociateNode (std::shared_ptr< N > nodeObject)=0 |
| void | dissociateNode (Nref nodeObject) |
| virtual void | dissociateEdge (std::shared_ptr< E > edgeObject)=0 |
| void | dissociateEdge (Eref edgeObject) |
| virtual void | dissociateEdge (std::shared_ptr< E > edgeObject)=0 |
| void | dissociateEdge (Eref edgeObject) |
| virtual NodeGraphid | getNodeGraphid (const std::shared_ptr< N > nodeObject) const=0 |
| NodeGraphid | getNodeGraphid (const Nref nodeObject) const |
| virtual NodeGraphid | getNodeGraphid (const std::shared_ptr< N > nodeObject) const=0 |
| NodeGraphid | getNodeGraphid (const Nref nodeObject) const |
| virtual EdgeGraphid | getEdgeGraphid (const std::shared_ptr< E > edgeObject) const=0 |
| EdgeGraphid | getEdgeGraphid (const Eref edgeObject) const |
| virtual EdgeGraphid | getEdgeGraphid (const std::shared_ptr< E > edgeObject) const=0 |
| EdgeGraphid | getEdgeGraphid (const Eref edgeObject) const |
| virtual const std::shared_ptr< N > | getNodeFromGraphid (NodeGraphid) const=0 |
| virtual std::shared_ptr< N > | getNodeFromGraphid (NodeGraphid)=0 |
| Nref | getNodeFromGraphid (NodeGraphid node) |
| const Nref | getNodeFromGraphid (NodeGraphid node) const |
| virtual const std::shared_ptr< N > | getNodeFromGraphid (NodeGraphid) const=0 |
| virtual std::shared_ptr< N > | getNodeFromGraphid (NodeGraphid)=0 |
| Nref | getNodeFromGraphid (NodeGraphid node) |
| const Nref | getNodeFromGraphid (NodeGraphid node) const |
| virtual std::vector< std::shared_ptr< N > > | getNodesFromGraphid (std::vector< NodeGraphid >) const=0 |
| std::vector< Nref > | getNodesFromGraphid (std::vector< NodeGraphid > nodes) const |
| virtual std::vector< std::shared_ptr< N > > | getNodesFromGraphid (std::vector< NodeGraphid >) const=0 |
| std::vector< Nref > | getNodesFromGraphid (std::vector< NodeGraphid > nodes) const |
| virtual std::shared_ptr< E > | getEdgeFromGraphid (EdgeGraphid)=0 |
| virtual const std::shared_ptr< E > | getEdgeFromGraphid (EdgeGraphid) const=0 |
| Eref | getEdgeFromGraphid (EdgeGraphid edge) |
| const Eref | getEdgeFromGraphid (EdgeGraphid edge) const |
| virtual std::shared_ptr< E > | getEdgeFromGraphid (EdgeGraphid)=0 |
| virtual const std::shared_ptr< E > | getEdgeFromGraphid (EdgeGraphid) const=0 |
| Eref | getEdgeFromGraphid (EdgeGraphid edge) |
| const Eref | getEdgeFromGraphid (EdgeGraphid edge) const |
| virtual std::vector< std::shared_ptr< E > > | getEdgesFromGraphid (std::vector< EdgeGraphid >) const=0 |
| std::vector< Eref > | getEdgesFromGraphid (std::vector< EdgeGraphid > edges) const |
| virtual std::vector< std::shared_ptr< E > > | getEdgesFromGraphid (std::vector< EdgeGraphid >) const=0 |
| std::vector< Eref > | getEdgesFromGraphid (std::vector< EdgeGraphid > edges) const |
| virtual std::shared_ptr< N > | getRoot () const=0 |
| Nref | getRoot () const |
| virtual std::shared_ptr< N > | getRoot () const=0 |
| Nref | getRoot () const |
| virtual NodeIndex | getRootIndex () const=0 |
| NodeIndex | getRootIndex () const |
| virtual NodeIndex | getRootIndex () const=0 |
| NodeIndex | getRootIndex () const |
| virtual bool | hasNodeIndex (const std::shared_ptr< N > nodeObject) const=0 |
| bool | hasNodeIndex (const Nref nodeObject) const |
| virtual bool | hasNodeIndex (const std::shared_ptr< N > nodeObject) const=0 |
| bool | hasNodeIndex (const Nref nodeObject) const |
| virtual bool | hasEdgeIndex (const std::shared_ptr< E > edgeObject) const=0 |
| bool | hasEdgeIndex (const Eref edgeObject) const |
| virtual bool | hasEdgeIndex (const std::shared_ptr< E > edgeObject) const=0 |
| bool | hasEdgeIndex (const Eref edgeObject) const |
| virtual NodeIndex | getNodeIndex (const std::shared_ptr< N > nodeObject) const=0 |
| NodeIndex | getNodeIndex (const Nref nodeObject) const |
| virtual NodeIndex | getNodeIndex (const std::shared_ptr< N > nodeObject) const=0 |
| NodeIndex | getNodeIndex (const Nref nodeObject) const |
| virtual std::vector< NodeIndex > | getNodeIndexes (std::vector< std::shared_ptr< N > > nodeObjects) const=0 |
| std::vector< NodeIndex > | getNodeIndexes (std::vector< Nref > nodes) const |
| virtual std::vector< NodeIndex > | getNodeIndexes (std::vector< std::shared_ptr< N > > nodeObjects) const=0 |
| std::vector< NodeIndex > | getNodeIndexes (std::vector< Nref > nodes) const |
| virtual EdgeIndex | getEdgeIndex (const std::shared_ptr< E > edgeObject) const=0 |
| EdgeIndex | getEdgeIndex (const Eref edgeObject) const |
| virtual EdgeIndex | getEdgeIndex (const std::shared_ptr< E > edgeObject) const=0 |
| EdgeIndex | getEdgeIndex (const Eref edgeObject) const |
| virtual std::vector< EdgeIndex > | getEdgeIndexes (std::vector< std::shared_ptr< E > > edgeObjects) const=0 |
| std::vector< EdgeIndex > | getEdgeIndexes (std::vector< Eref > edges) const |
| virtual std::vector< EdgeIndex > | getEdgeIndexes (std::vector< std::shared_ptr< E > > edgeObjects) const=0 |
| std::vector< EdgeIndex > | getEdgeIndexes (std::vector< Eref > edges) const |
| virtual NodeIndex | setNodeIndex (const std::shared_ptr< N > nodeObject, NodeIndex index)=0 |
| NodeIndex | setNodeIndex (const Nref nodeObject, NodeIndex index) |
| virtual NodeIndex | setNodeIndex (const std::shared_ptr< N > nodeObject, NodeIndex index)=0 |
| NodeIndex | setNodeIndex (const Nref nodeObject, NodeIndex index) |
| NodeIndex | setNodeIndex (const Nref nodeObject, NodeIndex index) |
| virtual EdgeIndex | setEdgeIndex (const std::shared_ptr< E > edgeObject, EdgeIndex index)=0 |
| EdgeIndex | setEdgeIndex (const Eref edgeObject, EdgeIndex index) |
| virtual EdgeIndex | setEdgeIndex (const std::shared_ptr< E > edgeObject, EdgeIndex index)=0 |
| EdgeIndex | setEdgeIndex (const Eref edgeObject, EdgeIndex index) |
| EdgeIndex | setEdgeIndex (const Eref edgeObject, EdgeIndex index) |
| virtual bool | hasNode (NodeIndex nodeIndex) const=0 |
| bool | hasNode (NodeIndex node) const |
| virtual bool | hasNode (NodeIndex nodeIndex) const=0 |
| bool | hasNode (Nref nodeObject) const |
| bool | hasNode (NodeIndex node) const |
| bool | hasNode (NodeIndex node) const |
| virtual bool | hasEdge (EdgeIndex edgeIndex) const=0 |
| bool | hasEdge (EdgeIndex edge) const |
| virtual bool | hasEdge (EdgeIndex edgeIndex) const=0 |
| bool | hasEdge (Eref edgeObject) const |
| bool | hasEdge (EdgeIndex edge) const |
| bool | hasEdge (EdgeIndex edge) const |
| virtual std::shared_ptr< N > | getNode (NodeIndex nodeIndex) const=0 |
| Nref | getNode (NodeIndex node) const |
| virtual std::shared_ptr< N > | getNode (NodeIndex nodeIndex) const=0 |
| Nref | getNode (NodeIndex node) const |
| Nref | getNode (NodeIndex node) const |
| virtual std::shared_ptr< E > | getEdge (EdgeIndex edgeIndex) const=0 |
| Eref | getEdge (EdgeIndex edge) const |
| virtual std::shared_ptr< E > | getEdge (EdgeIndex edgeIndex) const=0 |
| Eref | getEdge (EdgeIndex edge) const |
| Eref | getEdge (EdgeIndex edge) const |
| virtual std::unique_ptr< NodeIterator > | allNodesIterator ()=0 |
| virtual std::unique_ptr< NodeIterator > | allNodesIterator () const=0 |
| std::unique_ptr< typename AssociationGraphObserver< N, E >::NodeIterator > | allNodesIterator () |
| std::unique_ptr< typename AssociationGraphObserver< N, E >::NodeIterator > | allNodesIterator () const |
| virtual std::unique_ptr< NodeIterator > | allNodesIterator ()=0 |
| virtual std::unique_ptr< NodeIterator > | allNodesIterator () const=0 |
| std::unique_ptr< typename AssociationGraphObserver< N, E >::NodeIterator > | allNodesIterator () |
| std::unique_ptr< typename AssociationGraphObserver< N, E >::NodeIterator > | allNodesIterator () const |
| 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 |
| std::unique_ptr< typename AssociationGraphObserver< N, E >::NodeIterator > | outgoingNeighborNodesIterator (Nref node) |
| std::unique_ptr< typename AssociationGraphObserver< N, E >::NodeIterator > | outgoingNeighborNodesIterator (Nref node) const |
| 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 |
| std::unique_ptr< typename AssociationGraphObserver< N, E >::NodeIterator > | outgoingNeighborNodesIterator (Nref node) |
| std::unique_ptr< typename AssociationGraphObserver< N, E >::NodeIterator > | outgoingNeighborNodesIterator (Nref node) const |
| 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 |
| std::unique_ptr< typename AssociationGraphObserver< N, E >::NodeIterator > | incomingNeighborNodesIterator (Nref node) |
| std::unique_ptr< typename AssociationGraphObserver< N, E >::NodeIterator > | incomingNeighborNodesIterator (Nref node) const |
| 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 |
| std::unique_ptr< typename AssociationGraphObserver< N, E >::NodeIterator > | incomingNeighborNodesIterator (Nref node) |
| std::unique_ptr< typename AssociationGraphObserver< N, E >::NodeIterator > | incomingNeighborNodesIterator (Nref node) const |
| 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 |
| std::vector< Nref > | getNeighbors (const Nref node) const |
| std::vector< NodeIndex > | getNeighbors (NodeIndex node) const |
| 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 |
| std::vector< Nref > | getNeighbors (const Nref node) const |
| std::vector< NodeIndex > | getNeighbors (NodeIndex node) const |
| std::vector< NodeIndex > | getNeighbors (NodeIndex node) const |
| 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 |
| std::vector< Eref > | getEdges (const Nref node) const |
| std::vector< EdgeIndex > | getEdges (NodeIndex node) const |
| 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 |
| std::vector< Eref > | getEdges (const Nref node) const |
| std::vector< EdgeIndex > | getEdges (NodeIndex node) const |
| std::vector< EdgeIndex > | getEdges (NodeIndex node) const |
| 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 |
| std::vector< Nref > | getOutgoingNeighbors (const Nref node) const |
| std::vector< NodeIndex > | getOutgoingNeighbors (NodeIndex node) const |
| 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 |
| std::vector< Nref > | getOutgoingNeighbors (const Nref node) const |
| std::vector< NodeIndex > | getOutgoingNeighbors (NodeIndex node) const |
| std::vector< NodeIndex > | getOutgoingNeighbors (NodeIndex node) const |
| 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 |
| std::vector< Eref > | getOutgoingEdges (const Nref node) const |
| std::vector< EdgeIndex > | getOutgoingEdges (NodeIndex node) const |
| 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 |
| std::vector< Eref > | getOutgoingEdges (const Nref node) const |
| std::vector< EdgeIndex > | getOutgoingEdges (NodeIndex node) const |
| std::vector< EdgeIndex > | getOutgoingEdges (NodeIndex node) const |
| 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 |
| std::vector< Nref > | getIncomingNeighbors (const Nref node) const |
| std::vector< NodeIndex > | getIncomingNeighbors (NodeIndex node) const |
| 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 |
| std::vector< Nref > | getIncomingNeighbors (const Nref node) const |
| std::vector< NodeIndex > | getIncomingNeighbors (NodeIndex node) const |
| std::vector< NodeIndex > | getIncomingNeighbors (NodeIndex node) const |
| 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 |
| std::vector< Eref > | getIncomingEdges (const Nref node) const |
| std::vector< EdgeIndex > | getIncomingEdges (NodeIndex node) const |
| 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 |
| std::vector< Eref > | getIncomingEdges (const Nref node) const |
| std::vector< EdgeIndex > | getIncomingEdges (NodeIndex node) const |
| std::vector< EdgeIndex > | getIncomingEdges (NodeIndex node) const |
| virtual std::vector< std::shared_ptr< N > > | getLeavesFromNode (std::shared_ptr< N > node, unsigned int maxDepth) const=0 |
| std::vector< Nref > | getLeavesFromNode (Nref node, unsigned int maxDepth) const |
| virtual std::vector< std::shared_ptr< N > > | getLeavesFromNode (std::shared_ptr< N > node, unsigned int maxDepth) const=0 |
| std::vector< Nref > | getLeavesFromNode (Nref node, unsigned int maxDepth) const |
| virtual std::vector< std::shared_ptr< N > > | getAllLeaves () const=0 |
| std::vector< Nref > | getAllLeaves () const |
| virtual std::vector< std::shared_ptr< N > > | getAllLeaves () const=0 |
| std::vector< Nref > | getAllLeaves () const |
| virtual std::vector< NodeIndex > | getAllLeavesIndexes () const=0 |
| std::vector< NodeIndex > | getAllLeavesIndexes () const |
| virtual std::vector< NodeIndex > | getAllLeavesIndexes () const=0 |
| std::vector< NodeIndex > | getAllLeavesIndexes () const |
| virtual std::vector< std::shared_ptr< N > > | getAllInnerNodes () const=0 |
| std::vector< Nref > | getAllInnerNodes () const |
| virtual std::vector< std::shared_ptr< N > > | getAllInnerNodes () const=0 |
| std::vector< Nref > | getAllInnerNodes () const |
| virtual std::vector< NodeIndex > | getAllInnerNodesIndexes () const=0 |
| std::vector< NodeIndex > | getAllInnerNodesIndexes () const |
| virtual std::vector< NodeIndex > | getAllInnerNodesIndexes () const=0 |
| std::vector< NodeIndex > | getAllInnerNodesIndexes () const |
| virtual std::vector< std::shared_ptr< N > > | getAllNodes () const=0 |
| std::vector< Nref > | getAllNodes () const |
| virtual std::vector< std::shared_ptr< N > > | getAllNodes () const=0 |
| std::vector< Nref > | getAllNodes () const |
| virtual std::vector< NodeIndex > | getAllNodesIndexes () const=0 |
| std::vector< NodeIndex > | getAllNodesIndexes () const |
| virtual std::vector< NodeIndex > | getAllNodesIndexes () const=0 |
| std::vector< NodeIndex > | getAllNodesIndexes () const |
| virtual std::unique_ptr< EdgeIterator > | allEdgesIterator ()=0 |
| std::unique_ptr< typename AssociationGraphObserver< N, E >::EdgeIterator > | allEdgesIterator () |
| std::unique_ptr< typename AssociationGraphObserver< N, E >::EdgeIterator > | allEdgesIterator () const |
| virtual std::unique_ptr< EdgeIterator > | allEdgesIterator ()=0 |
| std::unique_ptr< typename AssociationGraphObserver< N, E >::EdgeIterator > | allEdgesIterator () |
| std::unique_ptr< typename AssociationGraphObserver< N, E >::EdgeIterator > | allEdgesIterator () const |
| virtual std::unique_ptr< EdgeIterator > | outgoingEdgesIterator (std::shared_ptr< N > node)=0 |
| std::unique_ptr< typename AssociationGraphObserver< N, E >::EdgeIterator > | outgoingEdgesIterator (Nref node) |
| std::unique_ptr< typename AssociationGraphObserver< N, E >::EdgeIterator > | outgoingEdgesIterator (Nref node) const |
| virtual std::unique_ptr< EdgeIterator > | outgoingEdgesIterator (std::shared_ptr< N > node)=0 |
| std::unique_ptr< typename AssociationGraphObserver< N, E >::EdgeIterator > | outgoingEdgesIterator (Nref node) |
| std::unique_ptr< typename AssociationGraphObserver< N, E >::EdgeIterator > | outgoingEdgesIterator (Nref node) const |
| virtual std::unique_ptr< EdgeIterator > | incomingEdgesIterator (std::shared_ptr< N > node)=0 |
| std::unique_ptr< typename AssociationGraphObserver< N, E >::EdgeIterator > | incomingEdgesIterator (Nref node) |
| std::unique_ptr< typename AssociationGraphObserver< N, E >::EdgeIterator > | incomingEdgesIterator (Nref node) const |
| virtual std::unique_ptr< EdgeIterator > | incomingEdgesIterator (std::shared_ptr< N > node)=0 |
| std::unique_ptr< typename AssociationGraphObserver< N, E >::EdgeIterator > | incomingEdgesIterator (Nref node) |
| std::unique_ptr< typename AssociationGraphObserver< N, E >::EdgeIterator > | incomingEdgesIterator (Nref node) const |
| virtual std::vector< std::shared_ptr< E > > | getAllEdges () const=0 |
| std::vector< Eref > | getAllEdges () const |
| virtual std::vector< std::shared_ptr< E > > | getAllEdges () const=0 |
| std::vector< Eref > | getAllEdges () const |
| virtual std::vector< EdgeIndex > | getAllEdgesIndexes () const=0 |
| std::vector< EdgeIndex > | getAllEdgesIndexes () const |
| virtual std::vector< EdgeIndex > | getAllEdgesIndexes () const=0 |
| std::vector< EdgeIndex > | getAllEdgesIndexes () const |
| virtual std::shared_ptr< E > | getEdgeLinking (std::shared_ptr< N > nodeA, std::shared_ptr< N > nodeB) const=0 |
| Eref | getEdgeLinking (Nref nodeA, Nref nodeB) const |
| virtual std::shared_ptr< E > | getEdgeLinking (std::shared_ptr< N > nodeA, std::shared_ptr< N > nodeB) const=0 |
| Eref | getEdgeLinking (Nref nodeA, Nref nodeB) const |
| virtual void | setEdgeLinking (std::shared_ptr< N > nodeA, std::shared_ptr< N > nodeB, std::shared_ptr< E > edge)=0 |
| void | setEdgeLinking (Nref nodeA, Nref nodeB, Eref edge) |
| virtual void | setEdgeLinking (std::shared_ptr< N > nodeA, std::shared_ptr< N > nodeB, std::shared_ptr< E > edge)=0 |
| void | setEdgeLinking (Nref nodeA, Nref nodeB, Eref edge) |
| virtual void | deletedEdgesUpdate (const std::vector< unsigned int > &edgesToDelete)=0 |
| void | deletedEdgesUpdate (const std::vector< unsigned int > &edgesToDelete) |
| virtual void | deletedEdgesUpdate (const std::vector< unsigned int > &edgesToDelete)=0 |
| void | deletedEdgesUpdate (const std::vector< unsigned int > &edgesToDelete) |
| virtual void | deletedNodesUpdate (const std::vector< unsigned int > &nodesToDelete)=0 |
| void | deletedNodesUpdate (const std::vector< unsigned int > &nodesToDelete) |
| virtual void | deletedNodesUpdate (const std::vector< unsigned int > &nodesToDelete)=0 |
| void | deletedNodesUpdate (const std::vector< unsigned int > &nodesToDelete) |
| NodeIndex | addNodeIndex (const Nref nodeObject) |
| NodeIndex | addNodeIndex (const Nref nodeObject) |
| EdgeIndex | addEdgeIndex (const Eref edgeObject) |
| EdgeIndex | addEdgeIndex (const Eref edgeObject) |
| void | setRoot (const Nref newRoot) |
| void | setRoot (const Nref newRoot) |
| void | outputToDot (const std::string &fname, const std::string &name) const |
| void | outputToDot (std::ostream &out, const std::string &name) const |
| void | outputToDot (const std::string &fname, const std::string &name) const |
| void | outputToDot (std::ostream &out, const std::string &name) const |
| bool | isLeaf (const Nref node) const |
| bool | isLeaf (const NodeIndex nodeid) const |
| bool | isLeaf (const Nref node) const |
| bool | isLeaf (const NodeIndex nodeid) const |
| bool | isLeaf (const NodeIndex nodeid) const |
| std::pair< Nref, Nref > | getNodes (Eref edge) const |
| std::pair< Nref, Nref > | getNodes (Eref edge) const |
| size_t | getNumberOfNodes () const |
| size_t | getNumberOfNodes () const |
| size_t | getNumberOfEdges () const |
| size_t | getNumberOfEdges () const |
| size_t | getNumberOfLeaves () const |
| size_t | getNumberOfLeaves () const |
| size_t | getDegree (const Nref node) const |
| size_t | getDegree (const Nref node) const |
| const std::shared_ptr< TreeGraphImpl > | getGraph () const |
| std::shared_ptr< TreeGraphImpl > | getGraph () |
| std::string | nodeToString (const Nref nodeObject) const |
| std::string | edgeToString (const Eref edgeObject) const |
| bool | hasParameter (const std::string &name) const override |
| const ParameterList & | getParameters () const override |
| const Parameter & | parameter (const std::string &name) const override |
| const std::shared_ptr< Parameter > & | getParameter (const std::string &name) const |
| double | getParameterValue (const std::string &name) const override |
| void | setAllParametersValues (const ParameterList ¶meters) override |
| void | setParameterValue (const std::string &name, double value) override |
| void | setParametersValues (const ParameterList ¶meters) override |
| bool | matchParametersValues (const ParameterList ¶meters) override |
| void | removeConstraint (const std::string &name) override |
| void | setConstraint (const std::string &name, std::shared_ptr< ConstraintInterface > constraint) override |
| size_t | getNumberOfParameters () const override |
| void | setNamespace (const std::string &prefix) override |
| std::string | getNamespace () const override |
| std::string | getParameterNameWithoutNamespace (const std::string &name) const override |
Static Public Member Functions | |
| 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) |
| 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) |
| 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) |
| 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) |
| 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) |
| 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) |
| 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) |
Protected Member Functions | |
| const std::shared_ptr< Parameter > & | getParameter (size_t i) const |
| std::shared_ptr< Parameter > & | getParameter (size_t i) |
| virtual void | addParameter_ (Parameter *parameter) |
| virtual void | addParameters_ (const ParameterList ¶meters) |
| virtual void | shareParameter_ (const std::shared_ptr< Parameter > ¶meter) |
| virtual void | shareParameters_ (const ParameterList ¶meters) |
| virtual void | includeParameters_ (const ParameterList ¶meters) |
| virtual void | deleteParameter_ (size_t index) |
| virtual void | deleteParameter_ (std::string &name) |
| virtual void | deleteParameters_ (const std::vector< std::string > &names) |
| void | resetParameters_ () |
| Parameter & | getParameter_ (const std::string &name) |
| Parameter & | getParameter_ (size_t index) |
| const Parameter & | getParameter_ (size_t index) const |
| Parameter & | getParameterWithNamespace_ (const std::string &name) |
| const Parameter & | getParameterWithNamespace_ (const std::string &name) const |
| ParameterList & | getParameters_ () override |
Protected Attributes | |
| std::shared_ptr< TreeGraphImpl > | subjectGraph_ |
Private Types | |
| enum | neighborType |
Private Member Functions | |
| void | fireParameterChanged (const ParameterList ¶meters) |
| std::vector< Nref > | getNeighbors_ (const Nref nodeObject, neighborType type) const |
| std::vector< Eref > | getEdges_ (const Nref nodeObject, neighborType type) const |
Private Attributes | |
| double | minimumBrLen_ |
| double | maximumBrLen_ |
| std::shared_ptr< ConstraintInterface > | brLenConstraint_ |
| INCOMING | |
| OUTGOING | |
| BOTH | |
| std::vector< Nref > | graphidToN_ |
| std::vector< Eref > | graphidToE_ |
| std::map< Nref, NodeGraphid > | NToGraphid_ |
| std::map< Eref, EdgeGraphid > | EToGraphid_ |
| std::vector< Nref > | indexToN_ |
| std::vector< Eref > | indexToE_ |
| std::map< Nref, NodeIndex > | NToIndex_ |
| std::map< Eref, EdgeIndex > | EToIndex_ |
| ParameterList | parameters_ |
| std::string | prefix_ |
Detailed Description
PhyloTree with Parametrizable Phylo Branches. They SHARE their branch length parameters.
Definition at line 24 of file ParametrizablePhyloTree.h.
Constructor & Destructor Documentation
◆ ParametrizablePhyloTree() [1/2]
| ParametrizablePhyloTree::ParametrizablePhyloTree | ( | const PhyloTree & | tree, |
| const std::string & | prefix = "" |
||
| ) |
Definition at line 10 of file ParametrizablePhyloTree.cpp.
References bpp::AssociationTreeGraphImplObserver< class, class, class >::getAllEdges(), bpp::AssociationTreeGraphImplObserver< class, class, class >::getEdgeIndex(), bpp::AssociationTreeGraphImplObserver< class, class, class >::hasEdgeIndex(), bpp::AbstractParametrizable::shareParameter_(), and bpp::TextTools::toString().
Referenced by clone().
◆ ParametrizablePhyloTree() [2/2]
| ParametrizablePhyloTree::ParametrizablePhyloTree | ( | const ParametrizablePhyloTree & | pTree | ) |
Definition at line 27 of file ParametrizablePhyloTree.cpp.
Member Function Documentation
◆ clone()
|
inlinevirtual |
Implements bpp::AbstractParametrizable.
Definition at line 40 of file ParametrizablePhyloTree.h.
References ParametrizablePhyloTree().
◆ fireParameterChanged()
|
privatevirtual |
Reimplemented from bpp::AbstractParametrizable.
Definition at line 78 of file ParametrizablePhyloTree.cpp.
◆ getAllLeavesNames()
| std::vector< std::string > ParametrizablePhyloTree::getAllLeavesNames | ( | ) | const |
Definition at line 51 of file ParametrizablePhyloTree.cpp.
References bpp::AssociationTreeGraphImplObserver< class, class, class >::getAllLeaves().
◆ getBranchLengths()
| Vdouble ParametrizablePhyloTree::getBranchLengths | ( | ) | const |
Definition at line 65 of file ParametrizablePhyloTree.cpp.
References bpp::AssociationTreeGraphImplObserver< class, class, class >::getAllEdges().
◆ getMaximumBranchLength()
|
inlinevirtual |
Definition at line 76 of file ParametrizablePhyloTree.h.
References maximumBrLen_.
◆ getMinimumBranchLength()
|
inlinevirtual |
Definition at line 75 of file ParametrizablePhyloTree.h.
References minimumBrLen_.
◆ operator=()
| ParametrizablePhyloTree & ParametrizablePhyloTree::operator= | ( | const ParametrizablePhyloTree & | pTree | ) |
Definition at line 36 of file ParametrizablePhyloTree.cpp.
References brLenConstraint_, maximumBrLen_, minimumBrLen_, and bpp::AssociationTreeGraphImplObserver< class, class, class >::operator=().
◆ setMaximumBranchLength()
|
inlinevirtual |
Definition at line 61 of file ParametrizablePhyloTree.h.
References brLenConstraint_, maximumBrLen_, minimumBrLen_, bpp::AbstractParametrizable::resetParameters_(), bpp::IntervalConstraint::setUpperBound(), and bpp::TextTools::toString().
◆ setMinimumBranchLength()
|
inlinevirtual |
Definition at line 47 of file ParametrizablePhyloTree.h.
References brLenConstraint_, maximumBrLen_, minimumBrLen_, bpp::AbstractParametrizable::resetParameters_(), bpp::IntervalConstraint::setLowerBound(), and bpp::TextTools::toString().
Member Data Documentation
◆ brLenConstraint_
|
private |
Definition at line 31 of file ParametrizablePhyloTree.h.
Referenced by operator=(), setMaximumBranchLength(), and setMinimumBranchLength().
◆ maximumBrLen_
|
private |
Definition at line 30 of file ParametrizablePhyloTree.h.
Referenced by getMaximumBranchLength(), operator=(), setMaximumBranchLength(), and setMinimumBranchLength().
◆ minimumBrLen_
|
private |
Definition at line 29 of file ParametrizablePhyloTree.h.
Referenced by getMinimumBranchLength(), operator=(), setMaximumBranchLength(), and setMinimumBranchLength().
The documentation for this class was generated from the following files:
- Bpp/Phyl/Likelihood/ParametrizablePhyloTree.h
- Bpp/Phyl/Likelihood/ParametrizablePhyloTree.cpp
