Likelihood ancestral states reconstruction: marginal method. More...

#include <Bpp/Phyl/Likelihood/MarginalAncestralReconstruction.h>

Inheritance diagram for bpp::MarginalAncestralReconstruction:

Collaboration diagram for bpp::MarginalAncestralReconstruction:

Public Member Functions
	MarginalAncestralReconstruction (std::shared_ptr< LikelihoodCalculationSingleProcess > drl)

	MarginalAncestralReconstruction (const MarginalAncestralReconstruction &masr)

MarginalAncestralReconstruction &	operator= (const MarginalAncestralReconstruction &masr)

MarginalAncestralReconstruction *	clone () const

virtual	~MarginalAncestralReconstruction ()

std::shared_ptr< const Alphabet >	getAlphabet () const

std::vector< size_t >	getAncestralStatesForNode (uint nodeId, VVdouble &probs, bool sample) const
	Get ancestral states for a given node as a vector of int. More...

std::vector< size_t >	getAncestralStatesForNode (uint nodeId) const override
	Get ancestral states for a given node as a vector of int. More...

std::map< uint, std::vector< size_t > >	getAllAncestralStates () const override
	Get all ancestral states for all nodes. More...

std::unique_ptr< Sequence >	getAncestralSequenceForNode (uint nodeId, VVdouble *probs, bool sample) const
	Get an ancestral sequence for a given node. More...

std::unique_ptr< Sequence >	getAncestralSequenceForNode (uint nodeId) const override
	Get the ancestral sequence for a given node. More...

std::unique_ptr< AlignedSequenceContainer >	getAncestralSequences () const override
	Get all the ancestral sequences for all nodes. More...

std::unique_ptr< AlignedSequenceContainer >	getAncestralSequences (bool sample) const

Private Member Functions
void	recursiveMarginalAncestralStates (const std::shared_ptr< PhyloNode > node, std::map< uint, std::vector< size_t >> &ancestors, AlignmentDataInterface &data) const

Private Attributes
std::shared_ptr< LikelihoodCalculationSingleProcess >	likelihood_

std::shared_ptr< const ParametrizablePhyloTree >	tree_

std::shared_ptr< const Alphabet >	alphabet_

size_t	nbSites_

size_t	nbDistinctSites_

size_t	nbStates_

PatternType	rootPatternLinks_

Detailed Description

Likelihood ancestral states reconstruction: marginal method.

Reference: Z Yang, S Kumar and M Nei (1995), Genetics 141(4) 1641-50.

Definition at line 29 of file MarginalAncestralReconstruction.h.

Constructor & Destructor Documentation

◆ MarginalAncestralReconstruction() [1/2]

bpp::MarginalAncestralReconstruction::MarginalAncestralReconstruction ( std::shared_ptr< LikelihoodCalculationSingleProcess > drl )

inline

Definition at line 43 of file MarginalAncestralReconstruction.h.

References tree_.

Referenced by clone().

◆ MarginalAncestralReconstruction() [2/2]

bpp::MarginalAncestralReconstruction::MarginalAncestralReconstruction ( const MarginalAncestralReconstruction & masr )

inline

Definition at line 56 of file MarginalAncestralReconstruction.h.

◆ ~MarginalAncestralReconstruction()

virtual bpp::MarginalAncestralReconstruction::~MarginalAncestralReconstruction ( )

inlinevirtual

Definition at line 81 of file MarginalAncestralReconstruction.h.

Member Function Documentation

◆ clone()

MarginalAncestralReconstruction* bpp::MarginalAncestralReconstruction::clone ( ) const

inline

Definition at line 79 of file MarginalAncestralReconstruction.h.

References MarginalAncestralReconstruction().

◆ getAllAncestralStates()

map< uint, vector< size_t > > MarginalAncestralReconstruction::getAllAncestralStates ( ) const

overridevirtual

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

Implements bpp::AncestralStateReconstruction.

Definition at line 55 of file MarginalAncestralReconstruction.cpp.

◆ getAlphabet()

std::shared_ptr<const Alphabet> bpp::MarginalAncestralReconstruction::getAlphabet ( ) const

inline

Definition at line 84 of file MarginalAncestralReconstruction.h.

References alphabet_.

◆ getAncestralSequenceForNode() [1/2]

std::unique_ptr<Sequence> bpp::MarginalAncestralReconstruction::getAncestralSequenceForNode ( uint nodeId ) const

inlineoverridevirtual

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.

Implements bpp::AncestralStateReconstruction.

Definition at line 138 of file MarginalAncestralReconstruction.h.

References getAncestralSequenceForNode().

◆ getAncestralSequenceForNode() [2/2]

unique_ptr< Sequence > MarginalAncestralReconstruction::getAncestralSequenceForNode	(	uint	nodeId,
		VVdouble *	probs,
		bool	sample
	)		const

Get an ancestral sequence for a given node.

The name of the sequence will be the name of the node if there is one, its id otherwise. A new sequence object is created, whose destruction is up to the user.

Parameters

nodeId	The id of the node at which the sequence must be reconstructed.
probs	A pointer toward a vector to be filled with the probability for each state at each site (set to NULL if you don't want these probabilities).
sample	Tell if the sequence should be sample from the posterior distribution instead of taking the one with maximum probability.

Returns: A sequence object.

Definition at line 64 of file MarginalAncestralReconstruction.cpp.

References bpp::TextTools::toString().

Referenced by getAncestralSequenceForNode().

◆ getAncestralSequences() [1/2]

std::unique_ptr<AlignedSequenceContainer> bpp::MarginalAncestralReconstruction::getAncestralSequences ( ) const

inlineoverridevirtual

Get all the ancestral sequences for all nodes.

Returns: A new SiteContainer object.

Implements bpp::AncestralStateReconstruction.

Definition at line 143 of file MarginalAncestralReconstruction.h.

◆ getAncestralSequences() [2/2]

unique_ptr< AlignedSequenceContainer > MarginalAncestralReconstruction::getAncestralSequences ( bool sample ) const

Definition at line 132 of file MarginalAncestralReconstruction.cpp.

◆ getAncestralStatesForNode() [1/2]

std::vector<size_t> bpp::MarginalAncestralReconstruction::getAncestralStatesForNode ( uint nodeId ) const

inlineoverridevirtual

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

Implements bpp::AncestralStateReconstruction.

Definition at line 111 of file MarginalAncestralReconstruction.h.

References getAncestralStatesForNode(), and nbSites_.

◆ getAncestralStatesForNode() [2/2]

vector< size_t > MarginalAncestralReconstruction::getAncestralStatesForNode	(	uint	nodeId,
		VVdouble &	probs,
		bool	sample
	)		const

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

The size of the vector is the total number of sites in the container associated to the likelihood object. 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 [in].
probs	A vector to be filled with the probability for each state at each position (will be the same size as the returned vector for states) [out].
sample	Tell if the sequence should be sampled from the posterior distribution instead of taking the one with maximum probability.

Returns: A vector of states indices.

See also: getAncestralSequenceForNode

Definition at line 13 of file MarginalAncestralReconstruction.cpp.

References bpp::copyEigenToBpp(), and bpp::RandomTools::giveRandomNumberBetweenZeroAndEntry().

Referenced by getAncestralStatesForNode().

◆ operator=()

MarginalAncestralReconstruction& bpp::MarginalAncestralReconstruction::operator= ( const MarginalAncestralReconstruction & masr )

inline

Definition at line 66 of file MarginalAncestralReconstruction.h.

References alphabet_, likelihood_, nbDistinctSites_, nbSites_, nbStates_, rootPatternLinks_, and tree_.

◆ recursiveMarginalAncestralStates()

void MarginalAncestralReconstruction::recursiveMarginalAncestralStates	(	const std::shared_ptr< PhyloNode >	node,
		std::map< uint, std::vector< size_t >> &	ancestors,
		AlignmentDataInterface &	data
	)		const