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

#include <Bpp/Phyl/Legacy/Likelihood/MarginalAncestralStateReconstruction.h>

Inheritance diagram for bpp::LegacyMarginalAncestralStateReconstruction:

Collaboration diagram for bpp::LegacyMarginalAncestralStateReconstruction:

Public Member Functions
	LegacyMarginalAncestralStateReconstruction (std::shared_ptr< const DRTreeLikelihoodInterface > drl)

	LegacyMarginalAncestralStateReconstruction (const LegacyMarginalAncestralStateReconstruction &masr)=default

LegacyMarginalAncestralStateReconstruction &	operator= (const LegacyMarginalAncestralStateReconstruction &masr)=default

LegacyMarginalAncestralStateReconstruction *	clone () const

virtual	~LegacyMarginalAncestralStateReconstruction ()

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

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

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

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

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

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

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

Private Member Functions
void	recursiveMarginalAncestralStates (const Node *node, std::map< int, std::vector< size_t >> &ancestors, AlignedSequenceContainer &data) const

Private Attributes
std::shared_ptr< const DRTreeLikelihoodInterface >	likelihood_

TreeTemplate< Node >	tree_

std::shared_ptr< const Alphabet >	alphabet_

size_t	nbSites_

size_t	nbDistinctSites_

size_t	nbClasses_

size_t	nbStates_

std::vector< size_t >	rootPatternLinks_

std::vector< double >	r_

std::vector< double >	l_

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 27 of file MarginalAncestralStateReconstruction.h.

Constructor & Destructor Documentation

◆ LegacyMarginalAncestralStateReconstruction() [1/2]

bpp::LegacyMarginalAncestralStateReconstruction::LegacyMarginalAncestralStateReconstruction ( std::shared_ptr< const DRTreeLikelihoodInterface > drl )

inline

Definition at line 43 of file MarginalAncestralStateReconstruction.h.

Referenced by clone().

◆ LegacyMarginalAncestralStateReconstruction() [2/2]

bpp::LegacyMarginalAncestralStateReconstruction::LegacyMarginalAncestralStateReconstruction ( const LegacyMarginalAncestralStateReconstruction & masr )

default

◆ ~LegacyMarginalAncestralStateReconstruction()

virtual bpp::LegacyMarginalAncestralStateReconstruction::~LegacyMarginalAncestralStateReconstruction ( )

inlinevirtual

Definition at line 62 of file MarginalAncestralStateReconstruction.h.

Member Function Documentation

◆ clone()

LegacyMarginalAncestralStateReconstruction* bpp::LegacyMarginalAncestralStateReconstruction::clone ( ) const

inline

Definition at line 60 of file MarginalAncestralStateReconstruction.h.

References LegacyMarginalAncestralStateReconstruction().

◆ getAllAncestralStates()

map< int, vector< size_t > > LegacyMarginalAncestralStateReconstruction::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::LegacyAncestralStateReconstruction.

Definition at line 69 of file MarginalAncestralStateReconstruction.cpp.

Referenced by bpp::LegacySubstitutionMappingTools::computeSubstitutionVectorsNoAveragingMarginal().

◆ getAncestralSequenceForNode() [1/2]

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

Definition at line 103 of file MarginalAncestralStateReconstruction.h.

References getAncestralSequenceForNode().

◆ getAncestralSequenceForNode() [2/2]

std::unique_ptr< Sequence > LegacyMarginalAncestralStateReconstruction::getAncestralSequenceForNode	(	int	nodeId,
		VVdouble *	probs,
		bool	sample
	)		const

Get the 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 78 of file MarginalAncestralStateReconstruction.cpp.

References bpp::TextTools::toString().

Referenced by getAncestralSequenceForNode().

◆ getAncestralSequences() [1/2]

std::unique_ptr<SiteContainerInterface> bpp::LegacyMarginalAncestralStateReconstruction::getAncestralSequences ( ) const

inlineoverridevirtual

Get all the ancestral sequences for all nodes.

Returns: A new SiteContainer object.

Implements bpp::LegacyAncestralStateReconstruction.

Definition at line 108 of file MarginalAncestralStateReconstruction.h.

◆ getAncestralSequences() [2/2]

unique_ptr< SiteContainerInterface > LegacyMarginalAncestralStateReconstruction::getAncestralSequences ( bool sample ) const

Definition at line 137 of file MarginalAncestralStateReconstruction.cpp.

◆ getAncestralStatesForNode() [1/2]

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

Definition at line 82 of file MarginalAncestralStateReconstruction.h.

References getAncestralStatesForNode(), and nbSites_.

◆ getAncestralStatesForNode() [2/2]

vector< size_t > LegacyMarginalAncestralStateReconstruction::getAncestralStatesForNode	(	int	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 number of distinct 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.
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).
sample	Tell if the sequence should be sample from the posterior distribution instead of taking the one with maximum probability.

Returns: A vector of states indices.

See also: getAncestralSequenceForNode

Definition at line 12 of file MarginalAncestralStateReconstruction.cpp.

References bpp::RandomTools::giveRandomNumberBetweenZeroAndEntry(), and bpp::VectorTools::whichMax().

Referenced by getAncestralStatesForNode().

◆ operator=()

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

default

◆ recursiveMarginalAncestralStates()

void LegacyMarginalAncestralStateReconstruction::recursiveMarginalAncestralStates	(	const Node *	node,
		std::map< int, std::vector< size_t >> &	ancestors,
		AlignedSequenceContainer &	data
	)		const