bpp-phyl3  3.0.0
bpp::AncestralStateReconstruction Class Referenceabstract

Interface for ancestral states reconstruction methods. More...

#include <Bpp/Phyl/AncestralStateReconstruction.h>

+ Inheritance diagram for bpp::AncestralStateReconstruction:

Public Member Functions

 AncestralStateReconstruction ()
 
virtual ~AncestralStateReconstruction ()
 
virtual std::vector< size_t > getAncestralStatesForNode (uint nodeId) const =0
 Get ancestral states for a given node as a vector of int. More...
 
virtual std::map< uint, std::vector< size_t > > getAllAncestralStates () const =0
 Get all ancestral states for all nodes. More...
 
virtual std::unique_ptr< SequencegetAncestralSequenceForNode (uint nodeId) const =0
 Get the ancestral sequence for a given node. More...
 
virtual std::unique_ptr< AlignedSequenceContainergetAncestralSequences () const =0
 Get all the ancestral sequences for all nodes. More...
 

Detailed Description

Interface for ancestral states reconstruction methods.

Definition at line 25 of file AncestralStateReconstruction.h.

Constructor & Destructor Documentation

◆ AncestralStateReconstruction()

bpp::AncestralStateReconstruction::AncestralStateReconstruction ( )
inline

Definition at line 28 of file AncestralStateReconstruction.h.

◆ ~AncestralStateReconstruction()

virtual bpp::AncestralStateReconstruction::~AncestralStateReconstruction ( )
inlinevirtual

Definition at line 29 of file AncestralStateReconstruction.h.

Member Function Documentation

◆ getAllAncestralStates()

virtual std::map<uint, std::vector<size_t> > bpp::AncestralStateReconstruction::getAllAncestralStates ( ) const
pure virtual

Get all ancestral states for all nodes.

Call the getAncestralSequenceForNode() method on each node in the tree.

Returns
A map with nodes id as key, and a vector of states indices as value.
See also
getAncestralSequenceForNode

Implemented in bpp::MarginalAncestralReconstruction.

◆ getAncestralSequenceForNode()

virtual std::unique_ptr<Sequence> bpp::AncestralStateReconstruction::getAncestralSequenceForNode ( uint  nodeId) const
pure virtual

Get the ancestral sequence for a given node.

Parameters
nodeIdThe id of the node at which the sequence must be reconstructed.
Returns
A sequence object.

Implemented in bpp::MarginalAncestralReconstruction.

◆ getAncestralSequences()

virtual std::unique_ptr<AlignedSequenceContainer> bpp::AncestralStateReconstruction::getAncestralSequences ( ) const
pure virtual

Get all the ancestral sequences for all nodes.

Returns
A new SiteContainer object.

Implemented in bpp::MarginalAncestralReconstruction.

◆ getAncestralStatesForNode()

virtual std::vector<size_t> bpp::AncestralStateReconstruction::getAncestralStatesForNode ( uint  nodeId) const
pure virtual

Get ancestral states for a given node as a vector of int.

The size of the vector depends on the implementation. This method is mainly for efficient internal use in other classes. Consider using the getAncestralSequenceForNode() method for a more general output.

Parameters
nodeIdthe id of the node at which the states must be reconstructed.
Returns
A vector of states indices.
See also
getAncestralSequenceForNode

Implemented in bpp::MarginalAncestralReconstruction.


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