bpp::AbstractDiscreteRatesAcrossSitesTreeLikelihood Class Reference

Partial implementation of the DiscreteRatesAcrossSitesTreeLikelihood interface. More...

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

Inheritance diagram for bpp::AbstractDiscreteRatesAcrossSitesTreeLikelihood:

Collaboration diagram for bpp::AbstractDiscreteRatesAcrossSitesTreeLikelihood:

Public Member Functions
	AbstractDiscreteRatesAcrossSitesTreeLikelihood (DiscreteDistribution *rDist, bool verbose=true) throw (Exception)
	AbstractDiscreteRatesAcrossSitesTreeLikelihood (const AbstractDiscreteRatesAcrossSitesTreeLikelihood &tl)
AbstractDiscreteRatesAcrossSitesTreeLikelihood &	operator= (const AbstractDiscreteRatesAcrossSitesTreeLikelihood &tl)
virtual	~AbstractDiscreteRatesAcrossSitesTreeLikelihood ()
TreeLikelihood *	clone () const =0
virtual void	setData (const SiteContainer &sites)=0
	Set the dataset for which the likelihood must be evaluated. More...
virtual TreeLikelihoodData *	getLikelihoodData ()=0
virtual const TreeLikelihoodData *	getLikelihoodData () const =0
virtual double	getLikelihoodForASite (size_t site) const =0
	Get the likelihood for a site. More...
virtual double	getLogLikelihoodForASite (size_t site) const =0
	Get the logarithm of the likelihood for a site. More...
virtual double	getLikelihood () const =0
	Get the likelihood for the whole dataset. More...
virtual double	getLogLikelihood () const =0
	Get the logarithm of the likelihood for the whole dataset. More...
virtual size_t	getNumberOfStates () const =0
virtual int	getAlphabetStateAsInt (size_t i) const =0
virtual std::string	getAlphabetStateAsChar (size_t i) const =0
virtual const std::vector< int > &	getAlphabetStates () const =0
virtual double	getLikelihoodForASiteForARateClass (size_t site, size_t rateClass) const =0
	Get the likelihood for a site knowing its rate class. More...
virtual double	getLogLikelihoodForASiteForARateClass (size_t site, size_t rateClass) const =0
	Get the logarithm of the likelihood for a site knowing its rate class. More...
virtual double	getLikelihoodForASiteForARateClassForAState (size_t site, size_t rateClass, int state) const =0
	Get the likelihood for a site knowing its rate class and its ancestral state. More...
virtual double	getLogLikelihoodForASiteForARateClassForAState (size_t site, size_t rateClass, int state) const =0
	Get the logarithm of the likelihood for a site knowing its rate class and its ancestral state. More...
virtual VVVdouble	getTransitionProbabilitiesPerRateClass (int nodeId, size_t siteIndex) const =0
	Retrieves all Pij(t) for a particular branch, defined by the upper node. More...
The TreeLikelihood interface.
Other methods are implemented in the AbstractTreeLikelihood class.
double	getLikelihoodForASiteForAState (size_t site, int state) const
	Get the likelihood for a site and for a state. More...
double	getLogLikelihoodForASiteForAState (size_t site, int state) const
	Get the logarithm of the likelihood for a site and for a state. More...
ParameterList	getDerivableParameters () const
	All derivable parameters. More...
ParameterList	getNonDerivableParameters () const
	All non derivable parameters. More...
VVdouble	getTransitionProbabilities (int nodeId, size_t siteIndex) const
	Retrieves all Pij(t) for a particular branch, defined by the upper node and site. More...
The DiscreteRatesAcrossSites interface implementation:
const DiscreteDistribution *	getRateDistribution () const
	Get the rate distribution used for the computation. More...
DiscreteDistribution *	getRateDistribution ()
	Get the rate distribution used for the computation. More...
size_t	getNumberOfClasses () const
	Get the number of classes. More...
ParameterList	getRateDistributionParameters () const
	Get the parameters associated to the rate distirbution. More...
VVdouble	getLikelihoodForEachSiteForEachRateClass () const
	Get the likelihood for each site and each rate class. More...
VVdouble	getLogLikelihoodForEachSiteForEachRateClass () const
	Get the logarithm of the likelihood for each site and each rate class. More...
VVVdouble	getLikelihoodForEachSiteForEachRateClassForEachState () const
	Get the likelihood for each site and each rate class and each state. More...
VVVdouble	getLogLikelihoodForEachSiteForEachRateClassForEachState () const
	Get the logarithm of the likelihood for each site and each rate class and each state. More...
VVdouble	getPosteriorProbabilitiesOfEachRate () const
	Get the posterior probability for each site of belonging to a particular rate class. More...
Vdouble	getRateWithMaxPostProbOfEachSite () const
	Get the posterior rate (the one with maximum posterior probability) for each site. More...
std::vector< size_t >	getRateClassWithMaxPostProbOfEachSite () const
	Get the posterior rate class (the one with maximum posterior probability) for each site. More...
Vdouble	getPosteriorRateOfEachSite () const
	Get the posterior rate, i.e. averaged over all classes and weighted with posterior probabilities, for each site. More...
The TreeLikelihood interface.
const SiteContainer *	getData () const
	Get the dataset for which the likelihood must be evaluated. More...
const Alphabet *	getAlphabet () const
	Get the alphabet associated to the dataset. More...
Vdouble	getLikelihoodForEachSite () const
	Get the likelihood for each site. More...
Vdouble	getLogLikelihoodForEachSite () const
	Get the logarithm of the likelihood for each site. More...
VVdouble	getLikelihoodForEachSiteForEachState () const
	Get the likelihood for each site and for each state. More...
VVdouble	getLogLikelihoodForEachSiteForEachState () const
	Get the logarithm of the likelihood for each site and for each state. More...
size_t	getNumberOfSites () const
	Get the number of sites in the dataset. More...
const Tree &	getTree () const
	Get the tree (topology and branch lengths). More...
void	enableDerivatives (bool yn)
	Tell if derivatives must be computed. More...
void	enableFirstOrderDerivatives (bool yn)
bool	enableFirstOrderDerivatives () const
void	enableSecondOrderDerivatives (bool yn)
bool	enableSecondOrderDerivatives () const
bool	isInitialized () const
void	initialize () throw (Exception)
	Init the likelihood object. More...
Retrieve some particular parameters subsets.
virtual ParameterList	getBranchLengthsParameters () const =0
	Get the branch lengths parameters. More...
virtual ParameterList	getSubstitutionModelParameters () const =0
	Get the parameters associated to substitution model(s). More...
virtual const SubstitutionModel *	getSubstitutionModel (int nodeId, size_t siteIndex) const =0 throw (NodeNotFoundException)
	Get the substitution model associated to a given node and alignment column. More...
virtual SubstitutionModel *	getSubstitutionModel (int nodeId, size_t siteIndex)=0 throw (NodeNotFoundException)
	Get the substitution model associated to a given node and alignment column. More...
virtual ConstBranchModelIterator *	getNewBranchModelIterator (int nodeId) const =0
virtual ConstSiteModelIterator *	getNewSiteModelIterator (size_t siteIndex) const =0
virtual size_t	getSiteIndex (size_t site) const =0 throw (IndexOutOfBoundsException)
	Get the index (used for inner computations) of a given site (original alignment column). More...
virtual const std::vector< double > &	getRootFrequencies (size_t siteIndex) const =0
	Get the values of the frequencies for each state in the alphabet at the root node. More...

Static Public Member Functions
Generic tools to deal with likelihood arrays
static void	resetLikelihoodArray (VVVdouble &likelihoodArray)
	Set all conditional likelihoods to 1. More...
static void	displayLikelihoodArray (const VVVdouble &likelihoodArray)
	Print the likelihood array to terminal (debugging tool). More...

Protected Attributes
DiscreteDistribution *	rateDistribution_
const SiteContainer *	data_
TreeTemplate< Node > *	tree_
bool	computeFirstOrderDerivatives_
bool	computeSecondOrderDerivatives_
bool	initialized_

Detailed Description

Partial implementation of the DiscreteRatesAcrossSitesTreeLikelihood interface.

It contains a pointer toward a DiscreteDistribution object. This object may be shared by several instances of the class.

Definition at line 56 of file AbstractDiscreteRatesAcrossSitesTreeLikelihood.h.

Constructor & Destructor Documentation

AbstractDiscreteRatesAcrossSitesTreeLikelihood() [1/2]

AbstractDiscreteRatesAcrossSitesTreeLikelihood::AbstractDiscreteRatesAcrossSitesTreeLikelihood	(	DiscreteDistribution *	rDist,
		bool	verbose = true
	)
throw	(	Exception
	)

Definition at line 53 of file AbstractDiscreteRatesAcrossSitesTreeLikelihood.cpp.

References bpp::AbstractTreeLikelihood::enableDerivatives().

AbstractDiscreteRatesAcrossSitesTreeLikelihood() [2/2]

bpp::AbstractDiscreteRatesAcrossSitesTreeLikelihood::AbstractDiscreteRatesAcrossSitesTreeLikelihood ( const AbstractDiscreteRatesAcrossSitesTreeLikelihood &  tl )

inline

Definition at line 69 of file AbstractDiscreteRatesAcrossSitesTreeLikelihood.h.

~AbstractDiscreteRatesAcrossSitesTreeLikelihood()

virtual bpp::AbstractDiscreteRatesAcrossSitesTreeLikelihood::~AbstractDiscreteRatesAcrossSitesTreeLikelihood ( )

inlinevirtual

Definition at line 83 of file AbstractDiscreteRatesAcrossSitesTreeLikelihood.h.

Member Function Documentation

clone()

TreeLikelihood* bpp::TreeLikelihood::clone ( ) const

pure virtualinherited

Implemented in bpp::NNIHomogeneousTreeLikelihood, bpp::RNonHomogeneousMixedTreeLikelihood, bpp::RNonHomogeneousTreeLikelihood, bpp::RHomogeneousTreeLikelihood, bpp::DRHomogeneousMixedTreeLikelihood, bpp::DRNonHomogeneousTreeLikelihood, bpp::DRHomogeneousTreeLikelihood, bpp::TwoTreeLikelihood, bpp::RHomogeneousMixedTreeLikelihood, bpp::RHomogeneousClockTreeLikelihood, bpp::DRTreeLikelihood, bpp::DiscreteRatesAcrossSitesClockTreeLikelihood, bpp::NonHomogeneousTreeLikelihood, bpp::ClockTreeLikelihood, bpp::HomogeneousTreeLikelihood, and bpp::SitePartitionHomogeneousTreeLikelihood.

displayLikelihoodArray()

void AbstractDiscreteRatesAcrossSitesTreeLikelihood::displayLikelihoodArray ( const VVVdouble &  likelihoodArray )

static

Print the likelihood array to terminal (debugging tool).

Parameters

likelihoodArray

the likelihood array.

Definition at line 287 of file AbstractDiscreteRatesAcrossSitesTreeLikelihood.cpp.

Referenced by bpp::DRHomogeneousTreeLikelihood::displayLikelihood(), bpp::DRNonHomogeneousTreeLikelihood::displayLikelihood(), bpp::RHomogeneousTreeLikelihood::displayLikelihood(), and bpp::RNonHomogeneousTreeLikelihood::displayLikelihood().

enableDerivatives()

void bpp::AbstractTreeLikelihood::enableDerivatives ( bool  yn )

inlinevirtualinherited

Tell if derivatives must be computed.

This methods calls the enableFirstOrderDerivatives and enableSecondOrderDerivatives.

Parameters

yn	Yes or no.

Implements bpp::TreeLikelihood.

Definition at line 292 of file AbstractTreeLikelihood.h.

References bpp::AbstractTreeLikelihood::computeFirstOrderDerivatives_, and bpp::AbstractTreeLikelihood::computeSecondOrderDerivatives_.

Referenced by AbstractDiscreteRatesAcrossSitesTreeLikelihood(), and bpp::DistanceEstimation::computeMatrix().

enableFirstOrderDerivatives() [1/2]

void bpp::AbstractTreeLikelihood::enableFirstOrderDerivatives ( bool  yn )

inlineinherited

Definition at line 293 of file AbstractTreeLikelihood.h.

References bpp::AbstractTreeLikelihood::computeFirstOrderDerivatives_.

enableFirstOrderDerivatives() [2/2]

bool bpp::AbstractTreeLikelihood::enableFirstOrderDerivatives ( ) const

inlineinherited

Definition at line 295 of file AbstractTreeLikelihood.h.

References bpp::AbstractTreeLikelihood::computeFirstOrderDerivatives_.

enableSecondOrderDerivatives() [1/2]

void bpp::AbstractTreeLikelihood::enableSecondOrderDerivatives ( bool  yn )

inlineinherited

Definition at line 294 of file AbstractTreeLikelihood.h.

References bpp::AbstractTreeLikelihood::computeFirstOrderDerivatives_, and bpp::AbstractTreeLikelihood::computeSecondOrderDerivatives_.

enableSecondOrderDerivatives() [2/2]

bool bpp::AbstractTreeLikelihood::enableSecondOrderDerivatives ( ) const

inlineinherited

Definition at line 296 of file AbstractTreeLikelihood.h.

References bpp::AbstractTreeLikelihood::computeSecondOrderDerivatives_.

getAlphabet()

const Alphabet* bpp::AbstractTreeLikelihood::getAlphabet ( ) const

inlinevirtualinherited

Get the alphabet associated to the dataset.

Returns

the alphabet associated to the dataset.

Implements bpp::TreeLikelihood.

Definition at line 285 of file AbstractTreeLikelihood.h.

References bpp::AbstractTreeLikelihood::data_.

getAlphabetStateAsChar()

virtual std::string bpp::TreeLikelihood::getAlphabetStateAsChar ( size_t  i ) const

pure virtualinherited

Returns

the alphabet state corresponding to the given model state.

Implemented in bpp::AbstractNonHomogeneousTreeLikelihood, bpp::AbstractHomogeneousTreeLikelihood, and bpp::TwoTreeLikelihood.

getAlphabetStateAsInt()

virtual int bpp::TreeLikelihood::getAlphabetStateAsInt ( size_t  i ) const

pure virtualinherited

Returns

the alphabet state corresponding to the given model state.

Implemented in bpp::AbstractNonHomogeneousTreeLikelihood, bpp::AbstractHomogeneousTreeLikelihood, and bpp::TwoTreeLikelihood.

getAlphabetStates()

virtual const std::vector<int>& bpp::TreeLikelihood::getAlphabetStates ( ) const

pure virtualinherited

Returns

the alphabet states corresponding to all model states.

Implemented in bpp::AbstractNonHomogeneousTreeLikelihood, bpp::AbstractHomogeneousTreeLikelihood, and bpp::TwoTreeLikelihood.

getBranchLengthsParameters()

virtual ParameterList bpp::TreeLikelihood::getBranchLengthsParameters ( ) const

pure virtualinherited

Get the branch lengths parameters.

Returns

A ParameterList with all branch lengths.

Implemented in bpp::AbstractNonHomogeneousTreeLikelihood, bpp::AbstractHomogeneousTreeLikelihood, and bpp::TwoTreeLikelihood.

Referenced by bpp::OptimizationTools::ScaleFunction::ScaleFunction().

getData()

const SiteContainer* bpp::AbstractTreeLikelihood::getData ( ) const

inlinevirtualinherited

Get the dataset for which the likelihood must be evaluated.

Returns

A pointer toward the site container where the sequences are stored.

Implements bpp::TreeLikelihood.

Definition at line 284 of file AbstractTreeLikelihood.h.

References bpp::AbstractTreeLikelihood::data_.

Referenced by bpp::RNonHomogeneousMixedTreeLikelihood::init().

getDerivableParameters()

ParameterList AbstractDiscreteRatesAcrossSitesTreeLikelihood::getDerivableParameters ( ) const

virtual

All derivable parameters.

Usually, this contains all branch lengths parameters.

Returns

A ParameterList.

Implements bpp::TreeLikelihood.

Reimplemented in bpp::RHomogeneousClockTreeLikelihood.

Definition at line 73 of file AbstractDiscreteRatesAcrossSitesTreeLikelihood.cpp.

getLikelihood()

virtual double bpp::TreeLikelihood::getLikelihood ( ) const

pure virtualinherited

Get the likelihood for the whole dataset.

Returns

The likelihood of the dataset.

Implemented in bpp::RNonHomogeneousTreeLikelihood, bpp::RHomogeneousTreeLikelihood, bpp::TwoTreeLikelihood, bpp::DRNonHomogeneousTreeLikelihood, bpp::DRHomogeneousTreeLikelihood, and bpp::DRHomogeneousMixedTreeLikelihood.

getLikelihoodData() [1/2]

virtual TreeLikelihoodData* bpp::TreeLikelihood::getLikelihoodData ( )

pure virtualinherited

Returns

The underlying likelihood data structure.

Implemented in bpp::RHomogeneousTreeLikelihood, bpp::RNonHomogeneousTreeLikelihood, bpp::DRNonHomogeneousTreeLikelihood, bpp::DRHomogeneousTreeLikelihood, bpp::TwoTreeLikelihood, and bpp::DRTreeLikelihood.

getLikelihoodData() [2/2]

virtual const TreeLikelihoodData* bpp::TreeLikelihood::getLikelihoodData ( ) const

pure virtualinherited

Returns

The underlying likelihood data structure.

Implemented in bpp::RHomogeneousTreeLikelihood, bpp::RNonHomogeneousTreeLikelihood, bpp::DRNonHomogeneousTreeLikelihood, bpp::DRHomogeneousTreeLikelihood, bpp::TwoTreeLikelihood, and bpp::DRTreeLikelihood.

getLikelihoodForASite()

virtual double bpp::TreeLikelihood::getLikelihoodForASite ( size_t  site ) const

pure virtualinherited

Get the likelihood for a site.

Parameters

site	The site index to analyse.

Returns

The likelihood for site site.

Implemented in bpp::RNonHomogeneousTreeLikelihood, bpp::RHomogeneousTreeLikelihood, bpp::TwoTreeLikelihood, bpp::DRNonHomogeneousTreeLikelihood, bpp::DRHomogeneousTreeLikelihood, and bpp::DRHomogeneousMixedTreeLikelihood.

Referenced by bpp::AbstractTreeLikelihood::getLikelihoodForEachSite().

getLikelihoodForASiteForARateClass()

virtual double bpp::DiscreteRatesAcrossSitesTreeLikelihood::getLikelihoodForASiteForARateClass ( size_t  site, size_t  rateClass  ) const

pure virtualinherited

Get the likelihood for a site knowing its rate class.

Parameters

site	The site index.
rateClass	The rate class index.

Returns

The likelihood for the specified site and rate class.

Implemented in bpp::RNonHomogeneousTreeLikelihood, bpp::TwoTreeLikelihood, bpp::RHomogeneousTreeLikelihood, bpp::DRNonHomogeneousTreeLikelihood, bpp::DRHomogeneousTreeLikelihood, bpp::DRHomogeneousMixedTreeLikelihood, and bpp::RHomogeneousMixedTreeLikelihood.

getLikelihoodForASiteForARateClassForAState()

virtual double bpp::DiscreteRatesAcrossSitesTreeLikelihood::getLikelihoodForASiteForARateClassForAState ( size_t  site, size_t  rateClass, int  state  ) const

pure virtualinherited

Get the likelihood for a site knowing its rate class and its ancestral state.

Parameters

site	The site index.
rateClass	The rate class index.
state	The ancestral state.

Returns

The likelihood for the specified site and rate class and ancestral state.

Implemented in bpp::RNonHomogeneousTreeLikelihood, bpp::TwoTreeLikelihood, bpp::RHomogeneousTreeLikelihood, bpp::DRNonHomogeneousTreeLikelihood, bpp::DRHomogeneousTreeLikelihood, bpp::DRHomogeneousMixedTreeLikelihood, and bpp::RHomogeneousMixedTreeLikelihood.

getLikelihoodForASiteForAState()

double AbstractDiscreteRatesAcrossSitesTreeLikelihood::getLikelihoodForASiteForAState ( size_t  site, int  state  ) const

virtual

Get the likelihood for a site and for a state.

Parameters

site	The site index to analyse.
state	The state to consider.

Returns

The likelihood for site site and state state.

Implements bpp::TreeLikelihood.

Definition at line 111 of file AbstractDiscreteRatesAcrossSitesTreeLikelihood.cpp.

getLikelihoodForEachSite()

Vdouble AbstractTreeLikelihood::getLikelihoodForEachSite ( ) const

virtualinherited

Get the likelihood for each site.

Returns

A vector with all likelihoods for each site.

Implements bpp::TreeLikelihood.

Definition at line 46 of file AbstractTreeLikelihood.cpp.

References bpp::TreeLikelihood::getLikelihoodForASite(), and bpp::AbstractTreeLikelihood::getNumberOfSites().

getLikelihoodForEachSiteForEachRateClass()

VVdouble AbstractDiscreteRatesAcrossSitesTreeLikelihood::getLikelihoodForEachSiteForEachRateClass ( ) const

virtual

Get the likelihood for each site and each rate class.

Returns

A two-dimension vector with all likelihoods.

Implements bpp::DiscreteRatesAcrossSitesTreeLikelihood.

Definition at line 93 of file AbstractDiscreteRatesAcrossSitesTreeLikelihood.cpp.

getLikelihoodForEachSiteForEachRateClassForEachState()

VVVdouble AbstractDiscreteRatesAcrossSitesTreeLikelihood::getLikelihoodForEachSiteForEachRateClassForEachState ( ) const

virtual

Get the likelihood for each site and each rate class and each state.

Returns

A three-dimension vector with all likelihoods.

Implements bpp::DiscreteRatesAcrossSitesTreeLikelihood.

Definition at line 156 of file AbstractDiscreteRatesAcrossSitesTreeLikelihood.cpp.

getLikelihoodForEachSiteForEachState()

VVdouble AbstractTreeLikelihood::getLikelihoodForEachSiteForEachState ( ) const

virtualinherited

Get the likelihood for each site and for each state.

Returns

A 2d vector with all likelihoods for each site and for each state.

Implements bpp::TreeLikelihood.

Definition at line 64 of file AbstractTreeLikelihood.cpp.

References bpp::TreeLikelihood::getLikelihoodForASiteForAState(), bpp::AbstractTreeLikelihood::getNumberOfSites(), and bpp::TreeLikelihood::getNumberOfStates().

getLogLikelihood()

virtual double bpp::TreeLikelihood::getLogLikelihood ( ) const

pure virtualinherited

Get the logarithm of the likelihood for the whole dataset.

Returns

The logarithm of the likelihood of the dataset.

Implemented in bpp::RNonHomogeneousTreeLikelihood, bpp::RHomogeneousTreeLikelihood, bpp::TwoTreeLikelihood, bpp::DRNonHomogeneousTreeLikelihood, bpp::DRHomogeneousTreeLikelihood, and bpp::DRHomogeneousMixedTreeLikelihood.

getLogLikelihoodForASite()

virtual double bpp::TreeLikelihood::getLogLikelihoodForASite ( size_t  site ) const

pure virtualinherited

Get the logarithm of the likelihood for a site.

Parameters

site	The site index to analyse.

Returns

The logarithm of the likelihood for site site.

Implemented in bpp::RNonHomogeneousTreeLikelihood, bpp::RHomogeneousTreeLikelihood, bpp::TwoTreeLikelihood, bpp::DRNonHomogeneousTreeLikelihood, bpp::DRHomogeneousTreeLikelihood, and bpp::DRHomogeneousMixedTreeLikelihood.

Referenced by bpp::AbstractTreeLikelihood::getLogLikelihoodForEachSite().

getLogLikelihoodForASiteForARateClass()

virtual double bpp::DiscreteRatesAcrossSitesTreeLikelihood::getLogLikelihoodForASiteForARateClass ( size_t  site, size_t  rateClass  ) const

pure virtualinherited

Get the logarithm of the likelihood for a site knowing its rate class.

Parameters

site	The site index.
rateClass	The rate class index.

Returns

The logarithm of the likelihood for the specified site and rate class.

Implemented in bpp::RNonHomogeneousTreeLikelihood, bpp::TwoTreeLikelihood, bpp::RHomogeneousTreeLikelihood, bpp::DRNonHomogeneousTreeLikelihood, bpp::DRHomogeneousTreeLikelihood, bpp::DRHomogeneousMixedTreeLikelihood, and bpp::RHomogeneousMixedTreeLikelihood.

getLogLikelihoodForASiteForARateClassForAState()

virtual double bpp::DiscreteRatesAcrossSitesTreeLikelihood::getLogLikelihoodForASiteForARateClassForAState ( size_t  site, size_t  rateClass, int  state  ) const

pure virtualinherited

Get the logarithm of the likelihood for a site knowing its rate class and its ancestral state.

Parameters

site	The site index.
rateClass	The rate class index.
state	The ancestral state.

Returns

The logarithm of the likelihood for the specified site and rate class and ancestral state..

Implemented in bpp::RNonHomogeneousTreeLikelihood, bpp::TwoTreeLikelihood, bpp::RHomogeneousTreeLikelihood, bpp::DRNonHomogeneousTreeLikelihood, bpp::DRHomogeneousTreeLikelihood, bpp::DRHomogeneousMixedTreeLikelihood, and bpp::RHomogeneousMixedTreeLikelihood.

getLogLikelihoodForASiteForAState()

double AbstractDiscreteRatesAcrossSitesTreeLikelihood::getLogLikelihoodForASiteForAState ( size_t  site, int  state  ) const

virtual

Get the logarithm of the likelihood for a site and for a state.

Parameters

site	The site index to analyse.
state	The state to consider.

Returns

The logarithm of the likelihood for site site and state state.

Implements bpp::TreeLikelihood.

Definition at line 124 of file AbstractDiscreteRatesAcrossSitesTreeLikelihood.cpp.

getLogLikelihoodForEachSite()

Vdouble AbstractTreeLikelihood::getLogLikelihoodForEachSite ( ) const

virtualinherited

Get the logarithm of the likelihood for each site.

Returns

A vector with all log likelihoods for each site.

Implements bpp::TreeLikelihood.

Definition at line 55 of file AbstractTreeLikelihood.cpp.

References bpp::TreeLikelihood::getLogLikelihoodForASite(), and bpp::AbstractTreeLikelihood::getNumberOfSites().

getLogLikelihoodForEachSiteForEachRateClass()

VVdouble AbstractDiscreteRatesAcrossSitesTreeLikelihood::getLogLikelihoodForEachSiteForEachRateClass ( ) const

virtual

Get the logarithm of the likelihood for each site and each rate class.

Returns

A two-dimension vector with all log likelihoods: V[i][j] = likelihood of site i and rate class j.

Implements bpp::DiscreteRatesAcrossSitesTreeLikelihood.

Definition at line 138 of file AbstractDiscreteRatesAcrossSitesTreeLikelihood.cpp.

getLogLikelihoodForEachSiteForEachRateClassForEachState()

VVVdouble AbstractDiscreteRatesAcrossSitesTreeLikelihood::getLogLikelihoodForEachSiteForEachRateClassForEachState ( ) const

virtual

Get the logarithm of the likelihood for each site and each rate class and each state.

Returns

A three-dimension vector with all log likelihoods: V[i][j][k} = likelihood of site i and rate class j and state k.

Implements bpp::DiscreteRatesAcrossSitesTreeLikelihood.

Definition at line 179 of file AbstractDiscreteRatesAcrossSitesTreeLikelihood.cpp.

getLogLikelihoodForEachSiteForEachState()

VVdouble AbstractTreeLikelihood::getLogLikelihoodForEachSiteForEachState ( ) const

virtualinherited

Get the logarithm of the likelihood for each site and for each state.

Returns

A 2d vector with all log likelihoods for each site and for each state.

Implements bpp::TreeLikelihood.

Definition at line 81 of file AbstractTreeLikelihood.cpp.

References bpp::TreeLikelihood::getLogLikelihoodForASiteForAState(), bpp::AbstractTreeLikelihood::getNumberOfSites(), and bpp::TreeLikelihood::getNumberOfStates().

getNewBranchModelIterator()

virtual ConstBranchModelIterator* bpp::TreeLikelihood::getNewBranchModelIterator ( int  nodeId ) const

pure virtualinherited

Implemented in bpp::AbstractNonHomogeneousTreeLikelihood, bpp::TwoTreeLikelihood, and bpp::AbstractHomogeneousTreeLikelihood.

getNewSiteModelIterator()

virtual ConstSiteModelIterator* bpp::TreeLikelihood::getNewSiteModelIterator ( size_t  siteIndex ) const

pure virtualinherited

Implemented in bpp::AbstractNonHomogeneousTreeLikelihood, bpp::TwoTreeLikelihood, and bpp::AbstractHomogeneousTreeLikelihood.

getNonDerivableParameters()

ParameterList AbstractDiscreteRatesAcrossSitesTreeLikelihood::getNonDerivableParameters ( ) const

virtual

All non derivable parameters.

Usually, this contains all substitution model parameters and rate distribution.

Returns

A ParameterList.

Implements bpp::TreeLikelihood.

Reimplemented in bpp::RHomogeneousClockTreeLikelihood.

Definition at line 82 of file AbstractDiscreteRatesAcrossSitesTreeLikelihood.cpp.

getNumberOfClasses()

size_t bpp::AbstractDiscreteRatesAcrossSitesTreeLikelihood::getNumberOfClasses ( ) const

inlinevirtual

Get the number of classes.

Returns

The Number of classes.

Implements bpp::DiscreteRatesAcrossSitesTreeLikelihood.

Definition at line 108 of file AbstractDiscreteRatesAcrossSitesTreeLikelihood.h.

References rateDistribution_.

getNumberOfSites()

size_t bpp::AbstractTreeLikelihood::getNumberOfSites ( ) const

inlinevirtualinherited

Get the number of sites in the dataset.

Returns

the number of sites in the dataset.

Implements bpp::TreeLikelihood.

Definition at line 290 of file AbstractTreeLikelihood.h.

References bpp::AbstractTreeLikelihood::data_.

Referenced by bpp::AbstractTreeLikelihood::getLikelihoodForEachSite(), bpp::AbstractTreeLikelihood::getLikelihoodForEachSiteForEachState(), bpp::AbstractTreeLikelihood::getLogLikelihoodForEachSite(), and bpp::AbstractTreeLikelihood::getLogLikelihoodForEachSiteForEachState().

getNumberOfStates()

virtual size_t bpp::TreeLikelihood::getNumberOfStates ( ) const

pure virtualinherited

Returns

the number of model states of the underlying Markov chain.

Implemented in bpp::AbstractNonHomogeneousTreeLikelihood, bpp::AbstractHomogeneousTreeLikelihood, and bpp::TwoTreeLikelihood.

Referenced by bpp::AbstractTreeLikelihood::getLikelihoodForEachSiteForEachState(), bpp::AbstractTreeLikelihood::getLogLikelihoodForEachSiteForEachState(), bpp::DRTreeLikelihoodTools::getPosteriorProbabilitiesForEachStateForEachRate(), and bpp::DRTreeLikelihoodTools::getPosteriorStateFrequencies().

getPosteriorProbabilitiesOfEachRate()

VVdouble AbstractDiscreteRatesAcrossSitesTreeLikelihood::getPosteriorProbabilitiesOfEachRate ( ) const

virtual

Get the posterior probability for each site of belonging to a particular rate class.

Returns

A two-dimension vector with all posterior probabilities: V[i][j] = probablity for site i of belonging to rate class j.

Implements bpp::DiscreteRatesAcrossSitesTreeLikelihood.

Definition at line 202 of file AbstractDiscreteRatesAcrossSitesTreeLikelihood.cpp.

getPosteriorRateOfEachSite()

Vdouble AbstractDiscreteRatesAcrossSitesTreeLikelihood::getPosteriorRateOfEachSite ( ) const

virtual

Get the posterior rate, i.e. averaged over all classes and weighted with posterior probabilities, for each site.

Returns

A vector with all rates.

Implements bpp::DiscreteRatesAcrossSitesTreeLikelihood.

Definition at line 220 of file AbstractDiscreteRatesAcrossSitesTreeLikelihood.cpp.

getRateClassWithMaxPostProbOfEachSite()

vector< size_t > AbstractDiscreteRatesAcrossSitesTreeLikelihood::getRateClassWithMaxPostProbOfEachSite ( ) const

virtual

Get the posterior rate class (the one with maximum posterior probability) for each site.

Returns

A vector with all rate classes indexes.

Implements bpp::DiscreteRatesAcrossSitesTreeLikelihood.

Definition at line 239 of file AbstractDiscreteRatesAcrossSitesTreeLikelihood.cpp.

getRateDistribution() [1/2]

const DiscreteDistribution* bpp::AbstractDiscreteRatesAcrossSitesTreeLikelihood::getRateDistribution ( ) const

inlinevirtual

Get the rate distribution used for the computation.

Returns

A const pointer toward the rate distribution of this instance.

Implements bpp::DiscreteRatesAcrossSitesTreeLikelihood.

Definition at line 106 of file AbstractDiscreteRatesAcrossSitesTreeLikelihood.h.

References rateDistribution_.

getRateDistribution() [2/2]

DiscreteDistribution* bpp::AbstractDiscreteRatesAcrossSitesTreeLikelihood::getRateDistribution ( )

inlinevirtual

Get the rate distribution used for the computation.

Returns

A pointer toward the rate distribution of this instance.

Implements bpp::DiscreteRatesAcrossSitesTreeLikelihood.

Definition at line 107 of file AbstractDiscreteRatesAcrossSitesTreeLikelihood.h.

References rateDistribution_.

getRateDistributionParameters()

ParameterList AbstractDiscreteRatesAcrossSitesTreeLikelihood::getRateDistributionParameters ( ) const

virtual

Get the parameters associated to the rate distirbution.

Returns

A ParameterList object with all rate distribution parameters.

Implements bpp::DiscreteRatesAcrossSitesTreeLikelihood.

Reimplemented in bpp::AbstractNonHomogeneousTreeLikelihood, and bpp::AbstractHomogeneousTreeLikelihood.

Definition at line 64 of file AbstractDiscreteRatesAcrossSitesTreeLikelihood.cpp.

Referenced by bpp::AbstractHomogeneousTreeLikelihood::getRateDistributionParameters(), and bpp::AbstractNonHomogeneousTreeLikelihood::getRateDistributionParameters().

getRateWithMaxPostProbOfEachSite()

Vdouble AbstractDiscreteRatesAcrossSitesTreeLikelihood::getRateWithMaxPostProbOfEachSite ( ) const

virtual

Get the posterior rate (the one with maximum posterior probability) for each site.

Returns

A vector with all rate classes indexes.

Implements bpp::DiscreteRatesAcrossSitesTreeLikelihood.

Definition at line 253 of file AbstractDiscreteRatesAcrossSitesTreeLikelihood.cpp.

getRootFrequencies()

virtual const std::vector<double>& bpp::TreeLikelihood::getRootFrequencies ( size_t  siteIndex ) const

pure virtualinherited

Get the values of the frequencies for each state in the alphabet at the root node.

For reversible models, these are the equilibrium frequencies. For non-reversible models, these usually are distinct parameters.

For models without site partitioning, the set of frequencies is the same for all positions. For partition models, the frequencies may differ from one site to another.

Parameters

siteIndex

The index of the alignment position.

See also

getSiteIndex

Returns

A vector with ancestral frequencies for each state in the alphabet;

Implemented in bpp::AbstractNonHomogeneousTreeLikelihood, bpp::AbstractHomogeneousTreeLikelihood, and bpp::TwoTreeLikelihood.

getSiteIndex()

virtual size_t bpp::TreeLikelihood::getSiteIndex ( size_t  site ) const throw ( IndexOutOfBoundsException )

pure virtualinherited

Get the index (used for inner computations) of a given site (original alignment column).

Parameters

site	An alignment position.

Returns

The site index corresponding to the given input alignment position.

Implemented in bpp::RHomogeneousTreeLikelihood, bpp::RNonHomogeneousTreeLikelihood, bpp::TwoTreeLikelihood, bpp::DRNonHomogeneousTreeLikelihood, and bpp::DRHomogeneousTreeLikelihood.

getSubstitutionModel() [1/2]

virtual const SubstitutionModel* bpp::TreeLikelihood::getSubstitutionModel ( int  nodeId, size_t  siteIndex  ) const throw ( NodeNotFoundException )

pure virtualinherited

Get the substitution model associated to a given node and alignment column.

Parameters

nodeId	The id of the request node.
siteIndex	The index of the alignment position.

See also

getSiteIndex

Returns

A pointer toward the corresponding model.

Exceptions

NodeNotFoundException

This exception may be thrown if the node is not found (depending on the implementation).

Implemented in bpp::AbstractHomogeneousTreeLikelihood, bpp::TwoTreeLikelihood, bpp::NonHomogeneousTreeLikelihood, bpp::HomogeneousTreeLikelihood, and bpp::SitePartitionHomogeneousTreeLikelihood.

getSubstitutionModel() [2/2]

virtual SubstitutionModel* bpp::TreeLikelihood::getSubstitutionModel ( int  nodeId, size_t  siteIndex  ) throw ( NodeNotFoundException )

pure virtualinherited

Get the substitution model associated to a given node and alignment column.

Parameters

nodeId	The id of the request node.
siteIndex	The index of the alignment position.

See also

getSiteIndex

Returns

A pointer toward the corresponding model.

Exceptions

NodeNotFoundException

This exception may be thrown if the node is not found (depending on the implementation).

Implemented in bpp::AbstractHomogeneousTreeLikelihood, bpp::TwoTreeLikelihood, bpp::NonHomogeneousTreeLikelihood, bpp::HomogeneousTreeLikelihood, and bpp::SitePartitionHomogeneousTreeLikelihood.

getSubstitutionModelParameters()

virtual ParameterList bpp::TreeLikelihood::getSubstitutionModelParameters ( ) const

pure virtualinherited

Get the parameters associated to substitution model(s).

Returns

A ParameterList.

Implemented in bpp::AbstractNonHomogeneousTreeLikelihood, bpp::AbstractHomogeneousTreeLikelihood, and bpp::TwoTreeLikelihood.

getTransitionProbabilities()

VVdouble AbstractDiscreteRatesAcrossSitesTreeLikelihood::getTransitionProbabilities ( int  nodeId, size_t  siteIndex  ) const

virtual

Retrieves all Pij(t) for a particular branch, defined by the upper node and site.

These intermediate results may be used by other methods.

Parameters

nodeId	The node defining the branch of interest.
siteIndex	The index of the alignment position.

See also

getSiteIndex

Returns

An array of dimension 2, where a[x][y] is the probability of substituting from x to y.

Implements bpp::TreeLikelihood.

Definition at line 311 of file AbstractDiscreteRatesAcrossSitesTreeLikelihood.cpp.

getTransitionProbabilitiesPerRateClass()

virtual VVVdouble bpp::DiscreteRatesAcrossSitesTreeLikelihood::getTransitionProbabilitiesPerRateClass ( int  nodeId, size_t  siteIndex  ) const

pure virtualinherited

Retrieves all Pij(t) for a particular branch, defined by the upper node.

These intermediate results may be used by other methods.

Parameters

nodeId	The node defining the branch of interest.
siteIndex	The position in the alignment.

Returns

An array of dimension 3, where a[c][x][y] is the probability of substituting from x to y while being in rate class c.

Implemented in bpp::AbstractNonHomogeneousTreeLikelihood, bpp::AbstractHomogeneousTreeLikelihood, and bpp::TwoTreeLikelihood.

getTree()

const Tree& bpp::AbstractTreeLikelihood::getTree ( ) const

inlinevirtualinherited

Get the tree (topology and branch lengths).

Returns

The tree of this TreeLikelihood object.

Implements bpp::TreeLikelihood.

Definition at line 291 of file AbstractTreeLikelihood.h.

References bpp::AbstractTreeLikelihood::tree_.

Referenced by bpp::NNIHomogeneousTreeLikelihood::getTopology(), and bpp::RNonHomogeneousMixedTreeLikelihood::init().

initialize()

void bpp::AbstractTreeLikelihood::initialize ( ) throw ( Exception )

inlinevirtualinherited

Init the likelihood object.

This method is used to initialize all parameters. It is typically called after the constructor and the setData method. It contains virtual methods that can't be called in the constructor.

Exceptions

Exception

if something bad happened, for instance if no data are associated to the likelihood function.

Implements bpp::TreeLikelihood.

Reimplemented in bpp::RNonHomogeneousMixedTreeLikelihood, bpp::DRHomogeneousMixedTreeLikelihood, and bpp::RHomogeneousMixedTreeLikelihood.

Definition at line 298 of file AbstractTreeLikelihood.h.

References bpp::AbstractTreeLikelihood::initialized_.

isInitialized()

bool bpp::AbstractTreeLikelihood::isInitialized ( ) const

inlinevirtualinherited

Returns

'true' is the likelihood function has been initialized.

Implements bpp::TreeLikelihood.

Definition at line 297 of file AbstractTreeLikelihood.h.

References bpp::AbstractTreeLikelihood::initialized_.

Referenced by bpp::DRHomogeneousTreeLikelihood::getValue(), bpp::DRNonHomogeneousTreeLikelihood::getValue(), bpp::RHomogeneousTreeLikelihood::getValue(), and bpp::RNonHomogeneousTreeLikelihood::getValue().

operator=()

AbstractDiscreteRatesAcrossSitesTreeLikelihood& bpp::AbstractDiscreteRatesAcrossSitesTreeLikelihood::operator= ( const AbstractDiscreteRatesAcrossSitesTreeLikelihood &  tl )

inline

Definition at line 75 of file AbstractDiscreteRatesAcrossSitesTreeLikelihood.h.

References bpp::AbstractTreeLikelihood::operator=(), and rateDistribution_.

Referenced by bpp::TwoTreeLikelihood::operator=(), bpp::AbstractHomogeneousTreeLikelihood::operator=(), and bpp::AbstractNonHomogeneousTreeLikelihood::operator=().

resetLikelihoodArray()

void AbstractDiscreteRatesAcrossSitesTreeLikelihood::resetLikelihoodArray ( VVVdouble &  likelihoodArray )

static

Set all conditional likelihoods to 1.

Parameters

likelihoodArray

the likelihood array.

Definition at line 267 of file AbstractDiscreteRatesAcrossSitesTreeLikelihood.cpp.

Referenced by bpp::DRHomogeneousTreeLikelihood::computeLikelihoodFromArrays(), bpp::DRNonHomogeneousTreeLikelihood::computeLikelihoodFromArrays(), bpp::DRHomogeneousTreeLikelihood::computeRootLikelihood(), bpp::DRNonHomogeneousTreeLikelihood::computeRootLikelihood(), bpp::DRHomogeneousTreeLikelihood::computeSubtreeLikelihoodPrefix(), bpp::DRNonHomogeneousTreeLikelihood::computeSubtreeLikelihoodPrefix(), bpp::DRHomogeneousTreeLikelihood::resetLikelihoodArrays(), and bpp::DRNonHomogeneousTreeLikelihood::resetLikelihoodArrays().

setData()

virtual void bpp::TreeLikelihood::setData ( const SiteContainer &  sites )

pure virtualinherited

Set the dataset for which the likelihood must be evaluated.

Parameters

sites

The data set to use.

Implemented in bpp::RNonHomogeneousMixedTreeLikelihood, bpp::NNIHomogeneousTreeLikelihood, bpp::TwoTreeLikelihood, bpp::RNonHomogeneousTreeLikelihood, bpp::RHomogeneousTreeLikelihood, bpp::DRNonHomogeneousTreeLikelihood, bpp::DRHomogeneousTreeLikelihood, bpp::DRHomogeneousMixedTreeLikelihood, and bpp::RHomogeneousMixedTreeLikelihood.

Member Data Documentation

computeFirstOrderDerivatives_

bool bpp::AbstractTreeLikelihood::computeFirstOrderDerivatives_

protectedinherited

Definition at line 227 of file AbstractTreeLikelihood.h.

Referenced by bpp::AbstractHomogeneousTreeLikelihood::computeTransitionProbabilitiesForNode(), bpp::RNonHomogeneousMixedTreeLikelihood::computeTransitionProbabilitiesForNode(), bpp::AbstractNonHomogeneousTreeLikelihood::computeTransitionProbabilitiesForNode(), bpp::AbstractTreeLikelihood::enableDerivatives(), bpp::AbstractTreeLikelihood::enableFirstOrderDerivatives(), bpp::AbstractTreeLikelihood::enableSecondOrderDerivatives(), bpp::DRHomogeneousTreeLikelihood::fireParameterChanged(), bpp::DRNonHomogeneousTreeLikelihood::fireParameterChanged(), bpp::TwoTreeLikelihood::fireParameterChanged(), and bpp::AbstractTreeLikelihood::operator=().

computeSecondOrderDerivatives_

bool bpp::AbstractTreeLikelihood::computeSecondOrderDerivatives_

protectedinherited

Definition at line 228 of file AbstractTreeLikelihood.h.

Referenced by bpp::AbstractHomogeneousTreeLikelihood::computeTransitionProbabilitiesForNode(), bpp::RNonHomogeneousMixedTreeLikelihood::computeTransitionProbabilitiesForNode(), bpp::AbstractNonHomogeneousTreeLikelihood::computeTransitionProbabilitiesForNode(), bpp::AbstractTreeLikelihood::enableDerivatives(), bpp::AbstractTreeLikelihood::enableSecondOrderDerivatives(), bpp::DRHomogeneousTreeLikelihood::fireParameterChanged(), bpp::DRNonHomogeneousTreeLikelihood::fireParameterChanged(), bpp::TwoTreeLikelihood::fireParameterChanged(), and bpp::AbstractTreeLikelihood::operator=().

data_

const SiteContainer* bpp::AbstractTreeLikelihood::data_

protectedinherited

Definition at line 225 of file AbstractTreeLikelihood.h.

Referenced by bpp::AbstractTreeLikelihood::AbstractTreeLikelihood(), bpp::AbstractTreeLikelihood::getAlphabet(), bpp::AbstractTreeLikelihood::getData(), bpp::AbstractTreeLikelihood::getNumberOfSites(), bpp::AbstractHomogeneousTreeLikelihood::initialize(), bpp::AbstractNonHomogeneousTreeLikelihood::initialize(), bpp::AbstractTreeLikelihood::operator=(), and bpp::AbstractTreeLikelihood::~AbstractTreeLikelihood().

initialized_

bool bpp::AbstractTreeLikelihood::initialized_

protectedinherited

Definition at line 229 of file AbstractTreeLikelihood.h.

Referenced by bpp::AbstractHomogeneousTreeLikelihood::applyParameters(), bpp::AbstractNonHomogeneousTreeLikelihood::applyParameters(), bpp::TwoTreeLikelihood::getBranchLengthsParameters(), bpp::AbstractHomogeneousTreeLikelihood::getBranchLengthsParameters(), bpp::AbstractNonHomogeneousTreeLikelihood::getBranchLengthsParameters(), bpp::TwoTreeLikelihood::getSubstitutionModelParameters(), bpp::AbstractHomogeneousTreeLikelihood::getSubstitutionModelParameters(), bpp::AbstractNonHomogeneousTreeLikelihood::getSubstitutionModelParameters(), bpp::TwoTreeLikelihood::initialize(), bpp::AbstractHomogeneousTreeLikelihood::initialize(), bpp::AbstractNonHomogeneousTreeLikelihood::initialize(), bpp::AbstractTreeLikelihood::initialize(), bpp::AbstractTreeLikelihood::isInitialized(), and bpp::AbstractTreeLikelihood::operator=().

rateDistribution_

DiscreteDistribution* bpp::AbstractDiscreteRatesAcrossSitesTreeLikelihood::rateDistribution_

protected

Definition at line 61 of file AbstractDiscreteRatesAcrossSitesTreeLikelihood.h.

Referenced by bpp::AbstractHomogeneousTreeLikelihood::applyParameters(), bpp::AbstractNonHomogeneousTreeLikelihood::applyParameters(), bpp::TwoTreeLikelihood::applyParameters(), bpp::DRHomogeneousTreeLikelihood::computeRootLikelihood(), bpp::DRNonHomogeneousTreeLikelihood::computeRootLikelihood(), bpp::AbstractHomogeneousTreeLikelihood::computeTransitionProbabilitiesForNode(), bpp::RNonHomogeneousMixedTreeLikelihood::computeTransitionProbabilitiesForNode(), bpp::AbstractNonHomogeneousTreeLikelihood::computeTransitionProbabilitiesForNode(), bpp::TwoTreeLikelihood::computeTreeD2Likelihood(), bpp::DRHomogeneousTreeLikelihood::computeTreeD2LikelihoodAtNode(), bpp::DRNonHomogeneousTreeLikelihood::computeTreeD2LikelihoodAtNode(), bpp::TwoTreeLikelihood::computeTreeDLikelihood(), bpp::DRHomogeneousTreeLikelihood::computeTreeDLikelihoodAtNode(), bpp::DRNonHomogeneousTreeLikelihood::computeTreeDLikelihoodAtNode(), bpp::TwoTreeLikelihood::computeTreeLikelihood(), bpp::DRHomogeneousTreeLikelihood::fireParameterChanged(), bpp::DRNonHomogeneousTreeLikelihood::fireParameterChanged(), bpp::RHomogeneousTreeLikelihood::fireParameterChanged(), bpp::RNonHomogeneousTreeLikelihood::fireParameterChanged(), bpp::TwoTreeLikelihood::fireParameterChanged(), bpp::RNonHomogeneousMixedTreeLikelihood::fireParameterChanged(), bpp::RNonHomogeneousTreeLikelihood::getD2LikelihoodForASite(), bpp::RHomogeneousTreeLikelihood::getD2LikelihoodForASite(), bpp::RNonHomogeneousTreeLikelihood::getDLikelihoodForASite(), bpp::RHomogeneousTreeLikelihood::getDLikelihoodForASite(), bpp::RHomogeneousTreeLikelihood::getLikelihoodForASite(), bpp::RNonHomogeneousTreeLikelihood::getLikelihoodForASite(), bpp::RHomogeneousTreeLikelihood::getLogLikelihoodForASite(), bpp::RNonHomogeneousTreeLikelihood::getLogLikelihoodForASite(), getNumberOfClasses(), getRateDistribution(), bpp::RNonHomogeneousMixedTreeLikelihood::init(), bpp::AbstractHomogeneousTreeLikelihood::initParameters(), bpp::AbstractNonHomogeneousTreeLikelihood::initParameters(), bpp::TwoTreeLikelihood::initParameters(), and operator=().

tree_

TreeTemplate<Node>* bpp::AbstractTreeLikelihood::tree_

mutableprotectedinherited

Definition at line 226 of file AbstractTreeLikelihood.h.

Referenced by bpp::AbstractHomogeneousTreeLikelihood::AbstractHomogeneousTreeLikelihood(), bpp::AbstractNonHomogeneousTreeLikelihood::AbstractNonHomogeneousTreeLikelihood(), bpp::AbstractTreeLikelihood::AbstractTreeLikelihood(), bpp::DRHomogeneousTreeLikelihood::computeLikelihoodAtNode(), bpp::DRNonHomogeneousTreeLikelihood::computeLikelihoodAtNode(), bpp::DRHomogeneousTreeLikelihood::computeRootLikelihood(), bpp::DRNonHomogeneousTreeLikelihood::computeRootLikelihood(), bpp::RNonHomogeneousTreeLikelihood::computeTreeD2Likelihood(), bpp::RNonHomogeneousMixedTreeLikelihood::computeTreeD2Likelihood(), bpp::RNonHomogeneousTreeLikelihood::computeTreeDLikelihood(), bpp::RNonHomogeneousMixedTreeLikelihood::computeTreeDLikelihood(), bpp::DRHomogeneousTreeLikelihood::computeTreeLikelihood(), bpp::DRNonHomogeneousTreeLikelihood::computeTreeLikelihood(), bpp::RNonHomogeneousTreeLikelihood::computeTreeLikelihood(), bpp::RHomogeneousTreeLikelihood::computeTreeLikelihood(), bpp::DRHomogeneousTreeLikelihood::DRHomogeneousTreeLikelihood(), bpp::DRNonHomogeneousTreeLikelihood::DRNonHomogeneousTreeLikelihood(), bpp::DRNonHomogeneousTreeLikelihood::fireParameterChanged(), bpp::RNonHomogeneousTreeLikelihood::fireParameterChanged(), bpp::RNonHomogeneousMixedTreeLikelihood::fireParameterChanged(), bpp::RNonHomogeneousTreeLikelihood::getD2LikelihoodForASiteForARateClass(), bpp::RHomogeneousTreeLikelihood::getD2LikelihoodForASiteForARateClass(), bpp::RNonHomogeneousTreeLikelihood::getDLikelihoodForASiteForARateClass(), bpp::RHomogeneousTreeLikelihood::getDLikelihoodForASiteForARateClass(), bpp::RHomogeneousTreeLikelihood::getLikelihoodForASiteForARateClass(), bpp::RNonHomogeneousTreeLikelihood::getLikelihoodForASiteForARateClass(), bpp::RHomogeneousTreeLikelihood::getLikelihoodForASiteForARateClassForAState(), bpp::RNonHomogeneousTreeLikelihood::getLikelihoodForASiteForARateClassForAState(), bpp::RHomogeneousTreeLikelihood::getLogLikelihoodForASiteForARateClass(), bpp::RNonHomogeneousTreeLikelihood::getLogLikelihoodForASiteForARateClass(), bpp::RHomogeneousTreeLikelihood::getLogLikelihoodForASiteForARateClassForAState(), bpp::RNonHomogeneousTreeLikelihood::getLogLikelihoodForASiteForARateClassForAState(), bpp::AbstractHomogeneousTreeLikelihood::getNewSiteModelIterator(), bpp::AbstractTreeLikelihood::getTree(), bpp::DRHomogeneousTreeLikelihood::operator=(), bpp::DRNonHomogeneousTreeLikelihood::operator=(), bpp::AbstractHomogeneousTreeLikelihood::operator=(), bpp::RHomogeneousTreeLikelihood::operator=(), bpp::RNonHomogeneousTreeLikelihood::operator=(), bpp::AbstractNonHomogeneousTreeLikelihood::operator=(), bpp::AbstractTreeLikelihood::operator=(), bpp::RHomogeneousTreeLikelihood::RHomogeneousTreeLikelihood(), bpp::RNonHomogeneousTreeLikelihood::RNonHomogeneousTreeLikelihood(), and bpp::AbstractTreeLikelihood::~AbstractTreeLikelihood().

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

• Bpp/Phyl/Likelihood/AbstractDiscreteRatesAcrossSitesTreeLikelihood.h
• Bpp/Phyl/Likelihood/AbstractDiscreteRatesAcrossSitesTreeLikelihood.cpp