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

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

Inheritance diagram for bpp::TreeLikelihoodTools:

Public Member Functions
	TreeLikelihoodTools ()

virtual	~TreeLikelihoodTools ()

Static Public Member Functions
static void	getAncestralFrequencies (const TreeLikelihood &tl, size_t site, std::map< int, std::vector< double > > &frequencies, bool alsoForLeaves=false) throw (Exception)
	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 TreeLikelihood &tl, std::map< int, std::vector< double > > &frequencies, bool alsoForLeaves=false) throw (Exception)
	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 TreeLikelihood &tl, size_t siteIndex, int parentId, const std::vector< double > &ancestralFrequencies, std::map< int, std::vector< double > > &frequencies, bool alsoForLeaves) throw (Exception)
	Recursive method, for internal use only. More...

Detailed Description

Utilitary methods that work with TreeLikelihood objects.

Definition at line 55 of file TreeLikelihoodTools.h.

Constructor & Destructor Documentation

◆ TreeLikelihoodTools()

bpp::TreeLikelihoodTools::TreeLikelihoodTools ( )

inline

Definition at line 58 of file TreeLikelihoodTools.h.

◆ ~TreeLikelihoodTools()

virtual bpp::TreeLikelihoodTools::~TreeLikelihoodTools ( )

inlinevirtual

Definition at line 59 of file TreeLikelihoodTools.h.

Member Function Documentation

◆ getAncestralFrequencies() [1/2]

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

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 unvalid model set.

Definition at line 45 of file TreeLikelihoodTools.cpp.

◆ getAncestralFrequencies() [2/2]

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

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 unvalid model set.

Definition at line 56 of file TreeLikelihoodTools.cpp.

◆ getAncestralFrequencies_()

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

staticprivate

Recursive method, for internal use only.

See also: getAncestralFrequencies()

Definition at line 94 of file TreeLikelihoodTools.cpp.

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

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

Public Member Functions

Static Public Member Functions

Static Private Member Functions