bpp::AncestralStateReconstruction Class Reference

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< Sequence >	getAncestralSequenceForNode (uint nodeId) const =0
	Get the ancestral sequence for a given node. More...
virtual std::unique_ptr< AlignedSequenceContainer >	getAncestralSequences () 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

nodeId

The 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

nodeId

the id of the node at which the states must be reconstructed.

Returns

A vector of states indices.

See also

getAncestralSequenceForNode

Implemented in bpp::MarginalAncestralReconstruction.

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

• Bpp/Phyl/AncestralStateReconstruction.h