bpp::LegacyAncestralStateReconstruction Class Reference

Interface for ancestral states reconstruction methods. More...

#include <Bpp/Phyl/Legacy/AncestralStateReconstruction.h>

Inheritance diagram for bpp::LegacyAncestralStateReconstruction:

Public Member Functions
	LegacyAncestralStateReconstruction ()
virtual	~LegacyAncestralStateReconstruction ()
virtual std::vector< size_t >	getAncestralStatesForNode (int nodeId) const =0
	Get ancestral states for a given node as a vector of int. More...
virtual std::map< int, std::vector< size_t > >	getAllAncestralStates () const =0
	Get all ancestral states for all nodes. More...
virtual std::unique_ptr< Sequence >	getAncestralSequenceForNode (int nodeId) const =0
	Get the ancestral sequence for a given node. More...
virtual std::unique_ptr< SiteContainerInterface >	getAncestralSequences () const =0
	Get all the ancestral sequences for all nodes. More...

Detailed Description

Interface for ancestral states reconstruction methods.

Definition at line 23 of file AncestralStateReconstruction.h.

Constructor & Destructor Documentation

LegacyAncestralStateReconstruction()

bpp::LegacyAncestralStateReconstruction::LegacyAncestralStateReconstruction ( )

inline

Definition at line 26 of file AncestralStateReconstruction.h.

~LegacyAncestralStateReconstruction()

virtual bpp::LegacyAncestralStateReconstruction::~LegacyAncestralStateReconstruction ( )

inlinevirtual

Definition at line 27 of file AncestralStateReconstruction.h.

Member Function Documentation

getAllAncestralStates()

virtual std::map<int, std::vector<size_t> > bpp::LegacyAncestralStateReconstruction::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::LegacyMarginalAncestralStateReconstruction.

getAncestralSequenceForNode()

virtual std::unique_ptr<Sequence> bpp::LegacyAncestralStateReconstruction::getAncestralSequenceForNode ( int  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::LegacyMarginalAncestralStateReconstruction.

getAncestralSequences()

virtual std::unique_ptr<SiteContainerInterface> bpp::LegacyAncestralStateReconstruction::getAncestralSequences ( ) const

pure virtual

Get all the ancestral sequences for all nodes.

Returns

A new SiteContainer object.

Implemented in bpp::LegacyMarginalAncestralStateReconstruction.

getAncestralStatesForNode()

virtual std::vector<size_t> bpp::LegacyAncestralStateReconstruction::getAncestralStatesForNode ( int  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::LegacyMarginalAncestralStateReconstruction.

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

• Bpp/Phyl/Legacy/AncestralStateReconstruction.h