Utilitary methods that work with TreeLikelihood objects. More...

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

Inheritance diagram for bpp::TreeLikelihoodTools:

Public Member Functions
	TreeLikelihoodTools ()

virtual	~TreeLikelihoodTools ()

Static Public Member Functions
static void	getAncestralFrequencies (const TreeLikelihoodInterface &tl, size_t site, std::map< int, std::vector< double >> &frequencies, bool alsoForLeaves=false)
	Compute the expected ancestral frequencies of all states at all (inner) nodes according to a Markov process defined by a given substitution model. More...

static void	getAncestralFrequencies (const TreeLikelihoodInterface &tl, std::map< int, std::vector< double >> &frequencies, bool alsoForLeaves=false)
	Compute the expected ancestral frequencies of all states at all (inner) nodes according to a Markov process defined by a given substitution model. More...

Static Private Member Functions
static void	getAncestralFrequencies_ (const TreeLikelihoodInterface &tl, size_t siteIndex, int parentId, const std::vector< double > &ancestralFrequencies, std::map< int, std::vector< double >> &frequencies, bool alsoForLeaves)
	Recursive method, for internal use only. More...

Detailed Description

Utilitary methods that work with TreeLikelihood objects.

Definition at line 20 of file TreeLikelihoodTools.h.

Constructor & Destructor Documentation

◆ TreeLikelihoodTools()

bpp::TreeLikelihoodTools::TreeLikelihoodTools ( )

inline

Definition at line 23 of file TreeLikelihoodTools.h.

◆ ~TreeLikelihoodTools()

virtual bpp::TreeLikelihoodTools::~TreeLikelihoodTools ( )

inlinevirtual

Definition at line 24 of file TreeLikelihoodTools.h.

Member Function Documentation

◆ getAncestralFrequencies() [1/2]

void TreeLikelihoodTools::getAncestralFrequencies	(	const TreeLikelihoodInterface &	tl,
		size_t	site,
		std::map< int, std::vector< double >> &	frequencies,
		bool	alsoForLeaves = `false`
	)

static

Compute the expected ancestral frequencies of all states at all (inner) nodes according to a Markov process defined by a given substitution model.

The computation is performed for a given site. If the likelihood object has no site partition, then the method will return the same result for all positions.

Parameters

tl	[in] A tree likelihood object.
site	[in] The site for which the frequencies should be computed.
frequencies	[out] A map where to store the results, as a vector of double (the size of which being equal to the number of states in the model), and with nodes id as keys.
alsoForLeaves	[opt] Tell if frequencies should also be estimated for terminal nodes.

Exceptions

Exception In case something bad happens, like an invalid model set.

Definition at line 10 of file TreeLikelihoodTools.cpp.

References bpp::TreeLikelihoodInterface::getRootFrequencies(), bpp::Tree::getRootId(), bpp::TreeLikelihoodInterface::getSiteIndex(), and bpp::TreeLikelihoodInterface::tree().

◆ getAncestralFrequencies() [2/2]

void TreeLikelihoodTools::getAncestralFrequencies	(	const TreeLikelihoodInterface &	tl,
		std::map< int, std::vector< double >> &	frequencies,
		bool	alsoForLeaves = `false`
	)

static

Compute the expected ancestral frequencies of all states at all (inner) nodes according to a Markov process defined by a given substitution model.

The computation is averaged over all sites. If the likelihood object has no site partition, then the method will return the same result as all single site numbers.

Parameters

tl	[in] A tree likelihood object.
frequencies	[out] A map where to store the results, as a vector of double (the size of which being equal to the number of states in the model), and with nodes id as keys.
alsoForLeaves	[opt] Tell if frequencies should also be estimated for terminal nodes.

Exceptions

Exception In case something bad happens, like an invalid model set.

Definition at line 21 of file TreeLikelihoodTools.cpp.

References bpp::TreeLikelihoodData::getNumberOfDistinctSites(), bpp::TreeLikelihoodInterface::getNumberOfStates(), bpp::TreeLikelihoodData::getWeight(), and bpp::TreeLikelihoodInterface::likelihoodData().

◆ getAncestralFrequencies_()

void TreeLikelihoodTools::getAncestralFrequencies_	(	const TreeLikelihoodInterface &	tl,
		size_t	siteIndex,
		int	parentId,
		const std::vector< double > &	ancestralFrequencies,
		std::map< int, std::vector< double >> &	frequencies,
		bool	alsoForLeaves
	)

staticprivate

Recursive method, for internal use only.

See also: getAncestralFrequencies()

Definition at line 63 of file TreeLikelihoodTools.cpp.

References bpp::TreeLikelihoodInterface::getNumberOfStates(), bpp::Tree::getSonsId(), bpp::TreeLikelihoodInterface::getTransitionProbabilities(), bpp::Tree::isLeaf(), and bpp::TreeLikelihoodInterface::tree().

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

Bpp/Phyl/Legacy/Likelihood/TreeLikelihoodTools.h
Bpp/Phyl/Legacy/Likelihood/TreeLikelihoodTools.cpp

Public Member Functions

Static Public Member Functions

Static Private Member Functions