bpp::TwoTreeLikelihood Class Reference

This class is a simplified version of DRHomogeneousTreeLikelihood for 2-Trees. More...

#include <Bpp/Phyl/Distance/DistanceEstimation.h>

Inheritance diagram for bpp::TwoTreeLikelihood:

Collaboration diagram for bpp::TwoTreeLikelihood:

Public Member Functions
	TwoTreeLikelihood (const std::string &seq1, const std::string &seq2, const SiteContainer &data, SubstitutionModel *model, DiscreteDistribution *rDist, bool verbose) throw (Exception)
	TwoTreeLikelihood (const TwoTreeLikelihood &lik)
TwoTreeLikelihood &	operator= (const TwoTreeLikelihood &lik)
TwoTreeLikelihood *	clone () const
virtual	~TwoTreeLikelihood ()
const SubstitutionModel *	getSubstitutionModel () const
	Get the substitution model used for the computation. More...
SubstitutionModel *	getSubstitutionModel ()
	Get the substitution model used for the computation. More...
ConstBranchModelIterator *	getNewBranchModelIterator (int nodeId) const throw (NotImplementedException)
ConstSiteModelIterator *	getNewSiteModelIterator (size_t siteIndex) const throw (NotImplementedException)
void	setParameters (const ParameterList &parameters) throw (ParameterNotFoundException, ConstraintException)
	Implements the Function interface. More...
double	getValue () const throw (Exception)
virtual void	initBranchLengthsParameters ()
virtual void	setMinimumBranchLength (double minimum)
virtual double	getMinimumBranchLength () const
The TreeLikelihood interface.
Other methods are implemented in the AbstractTreeLikelihood class.
size_t	getNumberOfStates () const
const std::vector< int > &	getAlphabetStates () const
int	getAlphabetStateAsInt (size_t i) const
std::string	getAlphabetStateAsChar (size_t i) const
TreeLikelihoodData *	getLikelihoodData () throw (NotImplementedException)
const TreeLikelihoodData *	getLikelihoodData () const throw (NotImplementedException)
double	getLikelihood () const
	Get the likelihood for the whole dataset. More...
double	getLogLikelihood () const
	Get the logarithm of the likelihood for the whole dataset. More...
double	getLikelihoodForASite (size_t site) const
	Get the likelihood for a site. More...
double	getLogLikelihoodForASite (size_t site) const
	Get the logarithm of the likelihood for a site. More...
ParameterList	getBranchLengthsParameters () const
	Get the branch lengths parameters. More...
ParameterList	getSubstitutionModelParameters () const
	Get the parameters associated to substitution model(s). More...
SubstitutionModel *	getSubstitutionModel (int nodeId, size_t siteIndex) throw (NodeNotFoundException)
	Get the substitution model associated to a given node and alignment column. More...
const SubstitutionModel *	getSubstitutionModel (int nodeId, size_t siteIndex) const throw (NodeNotFoundException)
	Get the substitution model associated to a given node and alignment column. More...
const std::vector< double > &	getRootFrequencies (size_t siteIndex) const
	Get the values of the frequencies for each state in the alphabet at the root node. More...
size_t	getSiteIndex (size_t site) const throw (IndexOutOfBoundsException)
	Get the index (used for inner computations) of a given site (original alignment column). More...
VVVdouble	getTransitionProbabilitiesPerRateClass (int nodeId, size_t siteIndex) const
	This method is not applicable for this object. More...
void	setData (const SiteContainer &sites) throw (Exception)
	Set the dataset for which the likelihood must be evaluated. More...
void	initialize () throw (Exception)
	Init the likelihood object. More...
The DiscreteRatesAcrossSites interface implementation:
double	getLikelihoodForASiteForARateClass (size_t site, size_t rateClass) const
	Get the likelihood for a site knowing its rate class. More...
double	getLogLikelihoodForASiteForARateClass (size_t site, size_t rateClass) const
	Get the logarithm of the likelihood for a site knowing its rate class. More...
double	getLikelihoodForASiteForARateClassForAState (size_t site, size_t rateClass, int state) const
	Get the likelihood for a site knowing its rate class and its ancestral state. More...
double	getLogLikelihoodForASiteForARateClassForAState (size_t site, size_t rateClass, int state) const
	Get the logarithm of the likelihood for a site knowing its rate class and its ancestral state. More...
DerivableFirstOrder interface.
double	getFirstOrderDerivative (const std::string &variable) const throw (Exception)
DerivableSecondOrder interface.
double	getSecondOrderDerivative (const std::string &variable) const throw (Exception)
double	getSecondOrderDerivative (const std::string &variable1, const std::string &variable2) const throw (Exception)
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

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 Member Functions
virtual void	initTreeLikelihoods (const SequenceContainer &sequences) throw (Exception)
	This method initializes the leaves according to a sequence container. More...
void	fireParameterChanged (const ParameterList &params)
virtual void	computeTreeLikelihood ()
virtual void	computeTreeDLikelihood ()
virtual void	computeTreeD2Likelihood ()
virtual void	initParameters ()
	This builds the parameters list from all parametrizable objects, i.e. substitution model, rate distribution and tree. More...
virtual void	applyParameters () throw (Exception)
	All parameters are stores in a parameter list. More...

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

Private Attributes
SiteContainer *	shrunkData_
std::vector< std::string >	seqnames_
SubstitutionModel *	model_
ParameterList	brLenParameters_
VVVdouble	pxy_
VVVdouble	dpxy_
VVVdouble	d2pxy_
std::vector< size_t >	rootPatternLinks_
	As previous, but for the global container. More...
std::vector< unsigned int >	rootWeights_
	The frequency of each site. More...
size_t	nbSites_
size_t	nbClasses_
size_t	nbStates_
size_t	nbDistinctSites_
VVVdouble	rootLikelihoods_
VVdouble	rootLikelihoodsS_
Vdouble	rootLikelihoodsSR_
Vdouble	dLikelihoods_
Vdouble	d2Likelihoods_
VVdouble	leafLikelihoods1_
VVdouble	leafLikelihoods2_
double	minimumBrLen_
Constraint *	brLenConstraint_
double	brLen_

Detailed Description

This class is a simplified version of DRHomogeneousTreeLikelihood for 2-Trees.

Definition at line 65 of file DistanceEstimation.h.

Constructor & Destructor Documentation

TwoTreeLikelihood() [1/2]

TwoTreeLikelihood::TwoTreeLikelihood	(	const std::string &	seq1,
		const std::string &	seq2,
		const SiteContainer &	data,
		SubstitutionModel *	model,
		DiscreteDistribution *	rDist,
		bool	verbose
	)
throw	(	Exception
	)

Definition at line 68 of file DistanceEstimation.cpp.

References bpp::SitePatterns::getIndices(), bpp::PatternTools::getSequenceSubset(), bpp::SitePatterns::getSites(), and bpp::SitePatterns::getWeights().

Referenced by clone().

TwoTreeLikelihood() [2/2]

TwoTreeLikelihood::TwoTreeLikelihood

(

const TwoTreeLikelihood &

lik

)

Definition at line 120 of file DistanceEstimation.cpp.

~TwoTreeLikelihood()

TwoTreeLikelihood::~TwoTreeLikelihood ( )

virtual

Definition at line 180 of file DistanceEstimation.cpp.

References brLenConstraint_, and shrunkData_.

Member Function Documentation

applyParameters()

void TwoTreeLikelihood::applyParameters ( ) throw ( Exception )

protectedvirtual

All parameters are stores in a parameter list.

This function apply these parameters to the substitution model, to the rate distribution and to the branch lengths.

Definition at line 297 of file DistanceEstimation.cpp.

References brLen_, model_, and bpp::AbstractDiscreteRatesAcrossSitesTreeLikelihood::rateDistribution_.

Referenced by fireParameterChanged().

clone()

TwoTreeLikelihood* bpp::TwoTreeLikelihood::clone ( ) const

inlinevirtual

Implements bpp::TreeLikelihood.

Definition at line 127 of file DistanceEstimation.h.

References TwoTreeLikelihood().

computeTreeD2Likelihood()

void TwoTreeLikelihood::computeTreeD2Likelihood ( )

protectedvirtual

Definition at line 559 of file DistanceEstimation.cpp.

References d2Likelihoods_, d2pxy_, bpp::SubstitutionModel::freq(), leafLikelihoods1_, leafLikelihoods2_, model_, nbClasses_, nbDistinctSites_, nbStates_, bpp::AbstractDiscreteRatesAcrossSitesTreeLikelihood::rateDistribution_, and rootLikelihoodsSR_.

Referenced by fireParameterChanged().

computeTreeDLikelihood()

void TwoTreeLikelihood::computeTreeDLikelihood ( )

protectedvirtual

Definition at line 528 of file DistanceEstimation.cpp.

References dLikelihoods_, dpxy_, bpp::SubstitutionModel::freq(), leafLikelihoods1_, leafLikelihoods2_, model_, nbClasses_, nbDistinctSites_, nbStates_, bpp::AbstractDiscreteRatesAcrossSitesTreeLikelihood::rateDistribution_, and rootLikelihoodsSR_.

Referenced by fireParameterChanged().

computeTreeLikelihood()

void TwoTreeLikelihood::computeTreeLikelihood ( )

protectedvirtual

Definition at line 477 of file DistanceEstimation.cpp.

References bpp::SubstitutionModel::getFrequencies(), leafLikelihoods1_, leafLikelihoods2_, model_, nbClasses_, nbDistinctSites_, nbStates_, pxy_, bpp::AbstractDiscreteRatesAcrossSitesTreeLikelihood::rateDistribution_, rootLikelihoods_, rootLikelihoodsS_, and rootLikelihoodsSR_.

Referenced by fireParameterChanged().

displayLikelihoodArray()

void AbstractDiscreteRatesAcrossSitesTreeLikelihood::displayLikelihoodArray ( const VVVdouble &  likelihoodArray )

staticinherited

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 bpp::AbstractDiscreteRatesAcrossSitesTreeLikelihood::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_.

fireParameterChanged()

void TwoTreeLikelihood::fireParameterChanged ( const ParameterList &  params )

protected

Definition at line 330 of file DistanceEstimation.cpp.

References applyParameters(), brLen_, bpp::AbstractTreeLikelihood::computeFirstOrderDerivatives_, bpp::AbstractTreeLikelihood::computeSecondOrderDerivatives_, computeTreeD2Likelihood(), computeTreeDLikelihood(), computeTreeLikelihood(), d2pxy_, dpxy_, bpp::SubstitutionModel::getd2Pij_dt2(), bpp::SubstitutionModel::getdPij_dt(), bpp::SubstitutionModel::getPij_t(), model_, nbClasses_, nbStates_, pxy_, and bpp::AbstractDiscreteRatesAcrossSitesTreeLikelihood::rateDistribution_.

Referenced by initialize().

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()

std::string bpp::TwoTreeLikelihood::getAlphabetStateAsChar ( size_t  i ) const

inlinevirtual

Returns

the alphabet state corresponding to the given model state.

Implements bpp::TreeLikelihood.

Definition at line 146 of file DistanceEstimation.h.

References bpp::SubstitutionModel::getAlphabetStateAsChar(), and model_.

getAlphabetStateAsInt()

int bpp::TwoTreeLikelihood::getAlphabetStateAsInt ( size_t  i ) const

inlinevirtual

Returns

the alphabet state corresponding to the given model state.

Implements bpp::TreeLikelihood.

Definition at line 144 of file DistanceEstimation.h.

References bpp::SubstitutionModel::getAlphabetStateAsInt(), and model_.

getAlphabetStates()

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

inlinevirtual

Returns

the alphabet states corresponding to all model states.

Implements bpp::TreeLikelihood.

Definition at line 142 of file DistanceEstimation.h.

References bpp::SubstitutionModel::getAlphabetStates(), and model_.

getBranchLengthsParameters()

ParameterList TwoTreeLikelihood::getBranchLengthsParameters ( ) const

virtual

Get the branch lengths parameters.

Returns

A ParameterList with all branch lengths.

Implements bpp::TreeLikelihood.

Definition at line 197 of file DistanceEstimation.cpp.

References brLenParameters_, and bpp::AbstractTreeLikelihood::initialized_.

Referenced by bpp::DistanceEstimation::computeMatrix().

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

virtualinherited

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.

getFirstOrderDerivative()

double TwoTreeLikelihood::getFirstOrderDerivative	(	const std::string &	variable	)	const
throw	(	Exception
	)

Definition at line 590 of file DistanceEstimation.cpp.

getLikelihood()

double TwoTreeLikelihood::getLikelihood ( ) const

virtual

Get the likelihood for the whole dataset.

Returns

The likelihood of the dataset.

Implements bpp::TreeLikelihood.

Definition at line 213 of file DistanceEstimation.cpp.

References nbDistinctSites_, rootLikelihoodsSR_, and rootWeights_.

getLikelihoodData() [1/2]

TreeLikelihoodData* bpp::TwoTreeLikelihood::getLikelihoodData ( ) throw ( NotImplementedException )

inlinevirtual

Returns

The underlying likelihood data structure.

Implements bpp::TreeLikelihood.

Definition at line 148 of file DistanceEstimation.h.

getLikelihoodData() [2/2]

const TreeLikelihoodData* bpp::TwoTreeLikelihood::getLikelihoodData ( ) const throw ( NotImplementedException )

inlinevirtual

Returns

The underlying likelihood data structure.

Implements bpp::TreeLikelihood.

Definition at line 152 of file DistanceEstimation.h.

getLikelihoodForASite()

double TwoTreeLikelihood::getLikelihoodForASite ( size_t  site ) const

virtual

Get the likelihood for a site.

Parameters

site	The site index to analyse.

Returns

The likelihood for site site.

Implements bpp::TreeLikelihood.

Definition at line 237 of file DistanceEstimation.cpp.

References rootLikelihoodsSR_, and rootPatternLinks_.

getLikelihoodForASiteForARateClass()

double TwoTreeLikelihood::getLikelihoodForASiteForARateClass ( size_t  site, size_t  rateClass  ) const

virtual

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.

Implements bpp::DiscreteRatesAcrossSitesTreeLikelihood.

Definition at line 251 of file DistanceEstimation.cpp.

References rootLikelihoodsS_, and rootPatternLinks_.

getLikelihoodForASiteForARateClassForAState()

double TwoTreeLikelihood::getLikelihoodForASiteForARateClassForAState ( size_t  site, size_t  rateClass, int  state  ) const

virtual

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.

Implements bpp::DiscreteRatesAcrossSitesTreeLikelihood.

Definition at line 265 of file DistanceEstimation.cpp.

References rootLikelihoods_, and rootPatternLinks_.

getLikelihoodForASiteForAState()

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

virtualinherited

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

virtualinherited

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

virtualinherited

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()

double TwoTreeLikelihood::getLogLikelihood ( ) const

virtual

Get the logarithm of the likelihood for the whole dataset.

Returns

The logarithm of the likelihood of the dataset.

Implements bpp::TreeLikelihood.

Definition at line 225 of file DistanceEstimation.cpp.

References nbDistinctSites_, rootLikelihoodsSR_, and rootWeights_.

Referenced by getValue().

getLogLikelihoodForASite()

double TwoTreeLikelihood::getLogLikelihoodForASite ( size_t  site ) const

virtual

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.

Implements bpp::TreeLikelihood.

Definition at line 244 of file DistanceEstimation.cpp.

References rootLikelihoodsSR_, and rootPatternLinks_.

getLogLikelihoodForASiteForARateClass()

double TwoTreeLikelihood::getLogLikelihoodForASiteForARateClass ( size_t  site, size_t  rateClass  ) const

virtual

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.

Implements bpp::DiscreteRatesAcrossSitesTreeLikelihood.

Definition at line 258 of file DistanceEstimation.cpp.

References rootLikelihoodsS_, and rootPatternLinks_.

getLogLikelihoodForASiteForARateClassForAState()

double TwoTreeLikelihood::getLogLikelihoodForASiteForARateClassForAState ( size_t  site, size_t  rateClass, int  state  ) const

virtual

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..

Implements bpp::DiscreteRatesAcrossSitesTreeLikelihood.

Definition at line 272 of file DistanceEstimation.cpp.

References rootLikelihoods_, and rootPatternLinks_.

getLogLikelihoodForASiteForAState()

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

virtualinherited

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

virtualinherited

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

virtualinherited

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().

getMinimumBranchLength()

virtual double bpp::TwoTreeLikelihood::getMinimumBranchLength ( ) const

inlinevirtual

Definition at line 254 of file DistanceEstimation.h.

References minimumBrLen_.

Referenced by bpp::DistanceEstimation::computeMatrix().

getNewBranchModelIterator()

ConstBranchModelIterator* bpp::TwoTreeLikelihood::getNewBranchModelIterator ( int  nodeId ) const throw ( NotImplementedException )

inlinevirtual

Implements bpp::TreeLikelihood.

Definition at line 199 of file DistanceEstimation.h.

getNewSiteModelIterator()

ConstSiteModelIterator* bpp::TwoTreeLikelihood::getNewSiteModelIterator ( size_t  siteIndex ) const throw ( NotImplementedException )

inlinevirtual

Implements bpp::TreeLikelihood.

Definition at line 204 of file DistanceEstimation.h.

getNonDerivableParameters()

ParameterList AbstractDiscreteRatesAcrossSitesTreeLikelihood::getNonDerivableParameters ( ) const

virtualinherited

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

inlinevirtualinherited

Get the number of classes.

Returns

The Number of classes.

Implements bpp::DiscreteRatesAcrossSitesTreeLikelihood.

Definition at line 108 of file AbstractDiscreteRatesAcrossSitesTreeLikelihood.h.

References bpp::AbstractDiscreteRatesAcrossSitesTreeLikelihood::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()

size_t bpp::TwoTreeLikelihood::getNumberOfStates ( ) const

inlinevirtual

Returns

the number of model states of the underlying Markov chain.

Implements bpp::TreeLikelihood.

Definition at line 140 of file DistanceEstimation.h.

References bpp::SubstitutionModel::getNumberOfStates(), and model_.

getPosteriorProbabilitiesOfEachRate()

VVdouble AbstractDiscreteRatesAcrossSitesTreeLikelihood::getPosteriorProbabilitiesOfEachRate ( ) const

virtualinherited

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

virtualinherited

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

virtualinherited

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

inlinevirtualinherited

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 bpp::AbstractDiscreteRatesAcrossSitesTreeLikelihood::rateDistribution_.

getRateDistribution() [2/2]

DiscreteDistribution* bpp::AbstractDiscreteRatesAcrossSitesTreeLikelihood::getRateDistribution ( )

inlinevirtualinherited

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 bpp::AbstractDiscreteRatesAcrossSitesTreeLikelihood::rateDistribution_.

getRateDistributionParameters()

ParameterList AbstractDiscreteRatesAcrossSitesTreeLikelihood::getRateDistributionParameters ( ) const

virtualinherited

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

virtualinherited

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()

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

inlinevirtual

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;

Implements bpp::TreeLikelihood.

Definition at line 164 of file DistanceEstimation.h.

References bpp::SubstitutionModel::getFrequencies(), and model_.

getSecondOrderDerivative() [1/2]

double TwoTreeLikelihood::getSecondOrderDerivative	(	const std::string &	variable	)	const
throw	(	Exception
	)

Definition at line 621 of file DistanceEstimation.cpp.

getSecondOrderDerivative() [2/2]

double bpp::TwoTreeLikelihood::getSecondOrderDerivative ( const std::string &  variable1, const std::string &  variable2  ) const throw ( Exception )

inline

Definition at line 241 of file DistanceEstimation.h.

getSiteIndex()

size_t bpp::TwoTreeLikelihood::getSiteIndex ( size_t  site ) const throw ( IndexOutOfBoundsException )

inlinevirtual

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.

Implements bpp::TreeLikelihood.

Definition at line 165 of file DistanceEstimation.h.

References rootPatternLinks_.

getSubstitutionModel() [1/4]

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

inlinevirtual

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).

Implements bpp::TreeLikelihood.

Definition at line 162 of file DistanceEstimation.h.

References model_.

getSubstitutionModel() [2/4]

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

inlinevirtual

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).

Implements bpp::TreeLikelihood.

Definition at line 163 of file DistanceEstimation.h.

References model_.

getSubstitutionModel() [3/4]

const SubstitutionModel* bpp::TwoTreeLikelihood::getSubstitutionModel ( ) const

inline

Get the substitution model used for the computation.

Returns

A const pointer toward the substitution model of this instance.

Definition at line 190 of file DistanceEstimation.h.

References model_.

getSubstitutionModel() [4/4]

SubstitutionModel* bpp::TwoTreeLikelihood::getSubstitutionModel ( )

inline

Get the substitution model used for the computation.

Returns

A pointer toward the substitution model of this instance.

Definition at line 197 of file DistanceEstimation.h.

References model_.

getSubstitutionModelParameters()

ParameterList TwoTreeLikelihood::getSubstitutionModelParameters ( ) const

virtual

Get the parameters associated to substitution model(s).

Returns

A ParameterList.

Implements bpp::TreeLikelihood.

Definition at line 205 of file DistanceEstimation.cpp.

References bpp::AbstractTreeLikelihood::initialized_, and model_.

getTransitionProbabilities()

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

virtualinherited

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()

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

inlinevirtual

This method is not applicable for this object.

Implements bpp::DiscreteRatesAcrossSitesTreeLikelihood.

Definition at line 169 of file DistanceEstimation.h.

References pxy_.

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().

getValue()

double TwoTreeLikelihood::getValue	(		)	const
throw	(	Exception
	)

Definition at line 411 of file DistanceEstimation.cpp.

References getLogLikelihood().

initBranchLengthsParameters()

void TwoTreeLikelihood::initBranchLengthsParameters ( )

virtual

Definition at line 309 of file DistanceEstimation.cpp.

References brLen_, brLenConstraint_, brLenParameters_, and minimumBrLen_.

Referenced by initParameters(), and setMinimumBranchLength().

initialize()

void TwoTreeLikelihood::initialize ( ) throw ( Exception )

virtual

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.

Definition at line 188 of file DistanceEstimation.cpp.

References fireParameterChanged(), bpp::AbstractTreeLikelihood::initialized_, and initParameters().

Referenced by bpp::DistanceEstimation::computeMatrix().

initParameters()

void TwoTreeLikelihood::initParameters ( )

protectedvirtual

This builds the parameters list from all parametrizable objects, i.e. substitution model, rate distribution and tree.

Definition at line 279 of file DistanceEstimation.cpp.

References brLenParameters_, initBranchLengthsParameters(), model_, and bpp::AbstractDiscreteRatesAcrossSitesTreeLikelihood::rateDistribution_.

Referenced by initialize().

initTreeLikelihoods()

void TwoTreeLikelihood::initTreeLikelihoods ( const SequenceContainer &  sequences ) throw ( Exception )

protectedvirtual

This method initializes the leaves according to a sequence container.

Here the container shrunkData_ is used. Likelihood is set to 1 for the state corresponding to the sequence site, otherwise it is set to 0.

The two likelihood arrays are initialized according to alphabet size and sequences length, and filled with 1.

NB: This method is recursive.

Parameters

sequences

The sequence container to use.

Definition at line 419 of file DistanceEstimation.cpp.

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=()

TwoTreeLikelihood & TwoTreeLikelihood::operator=

(

const TwoTreeLikelihood &

lik

)

Definition at line 149 of file DistanceEstimation.cpp.

References brLen_, brLenConstraint_, brLenParameters_, d2Likelihoods_, d2pxy_, dLikelihoods_, dpxy_, leafLikelihoods1_, leafLikelihoods2_, minimumBrLen_, model_, nbClasses_, nbDistinctSites_, nbSites_, nbStates_, bpp::AbstractDiscreteRatesAcrossSitesTreeLikelihood::operator=(), pxy_, rootLikelihoods_, rootLikelihoodsS_, rootLikelihoodsSR_, rootPatternLinks_, rootWeights_, seqnames_, and shrunkData_.

resetLikelihoodArray()

void AbstractDiscreteRatesAcrossSitesTreeLikelihood::resetLikelihoodArray ( VVVdouble &  likelihoodArray )

staticinherited

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()

void bpp::TwoTreeLikelihood::setData ( const SiteContainer &  sites ) throw ( Exception )

inlinevirtual

Set the dataset for which the likelihood must be evaluated.

Parameters

sites

The data set to use.

Implements bpp::TreeLikelihood.

Definition at line 170 of file DistanceEstimation.h.

setMinimumBranchLength()

virtual void bpp::TwoTreeLikelihood::setMinimumBranchLength ( double  minimum )

inlinevirtual

Definition at line 246 of file DistanceEstimation.h.

References brLenConstraint_, initBranchLengthsParameters(), and minimumBrLen_.

setParameters()

void TwoTreeLikelihood::setParameters	(	const ParameterList &	parameters	)
throw	(	ParameterNotFoundException,
		ConstraintException
	)

Implements the Function interface.

Update the parameter list and call the applyParameters() method. Then compute the likelihoods at each node (computeLikelihood() method) and call the getLogLikelihood() method.

If a subset of the whole parameter list is passed to the function, only these parameters are updated and the other remain constant (i.e. equal to their last value).

Parameters

parameters

The parameter list to pass to the function.

Definition at line 322 of file DistanceEstimation.cpp.

Member Data Documentation

brLen_

double bpp::TwoTreeLikelihood::brLen_

private

Definition at line 113 of file DistanceEstimation.h.

Referenced by applyParameters(), fireParameterChanged(), initBranchLengthsParameters(), and operator=().

brLenConstraint_

Constraint* bpp::TwoTreeLikelihood::brLenConstraint_

private

Definition at line 112 of file DistanceEstimation.h.

Referenced by initBranchLengthsParameters(), operator=(), setMinimumBranchLength(), and ~TwoTreeLikelihood().

brLenParameters_

ParameterList bpp::TwoTreeLikelihood::brLenParameters_

private

Definition at line 72 of file DistanceEstimation.h.

Referenced by getBranchLengthsParameters(), initBranchLengthsParameters(), initParameters(), and operator=().

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(), 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(), fireParameterChanged(), and bpp::AbstractTreeLikelihood::operator=().

d2Likelihoods_

Vdouble bpp::TwoTreeLikelihood::d2Likelihoods_

mutableprivate

Definition at line 108 of file DistanceEstimation.h.

Referenced by computeTreeD2Likelihood(), and operator=().

d2pxy_

VVVdouble bpp::TwoTreeLikelihood::d2pxy_

mutableprivate

Definition at line 78 of file DistanceEstimation.h.

Referenced by computeTreeD2Likelihood(), fireParameterChanged(), and 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().

dLikelihoods_

Vdouble bpp::TwoTreeLikelihood::dLikelihoods_

mutableprivate

Definition at line 107 of file DistanceEstimation.h.

Referenced by computeTreeDLikelihood(), and operator=().

dpxy_

VVVdouble bpp::TwoTreeLikelihood::dpxy_

mutableprivate

Definition at line 76 of file DistanceEstimation.h.

Referenced by computeTreeDLikelihood(), fireParameterChanged(), and operator=().

initialized_

bool bpp::AbstractTreeLikelihood::initialized_

protectedinherited

Definition at line 229 of file AbstractTreeLikelihood.h.

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

leafLikelihoods1_

VVdouble bpp::TwoTreeLikelihood::leafLikelihoods1_

mutableprivate

Definition at line 109 of file DistanceEstimation.h.

Referenced by computeTreeD2Likelihood(), computeTreeDLikelihood(), computeTreeLikelihood(), and operator=().

leafLikelihoods2_

VVdouble bpp::TwoTreeLikelihood::leafLikelihoods2_

mutableprivate

Definition at line 109 of file DistanceEstimation.h.

Referenced by computeTreeD2Likelihood(), computeTreeDLikelihood(), computeTreeLikelihood(), and operator=().

minimumBrLen_

double bpp::TwoTreeLikelihood::minimumBrLen_

private

Definition at line 111 of file DistanceEstimation.h.

Referenced by getMinimumBranchLength(), initBranchLengthsParameters(), operator=(), and setMinimumBranchLength().

model_

SubstitutionModel* bpp::TwoTreeLikelihood::model_

private

Definition at line 71 of file DistanceEstimation.h.

Referenced by applyParameters(), computeTreeD2Likelihood(), computeTreeDLikelihood(), computeTreeLikelihood(), fireParameterChanged(), getAlphabetStateAsChar(), getAlphabetStateAsInt(), getAlphabetStates(), getNumberOfStates(), getRootFrequencies(), getSubstitutionModel(), bpp::DistanceEstimation::getSubstitutionModel(), getSubstitutionModelParameters(), bpp::DistanceEstimation::hasSubstitutionModel(), bpp::DistanceEstimation::init_(), initParameters(), operator=(), bpp::DistanceEstimation::operator=(), and bpp::DistanceEstimation::resetSubstitutionModel().

nbClasses_

size_t bpp::TwoTreeLikelihood::nbClasses_

private

Definition at line 99 of file DistanceEstimation.h.

Referenced by computeTreeD2Likelihood(), computeTreeDLikelihood(), computeTreeLikelihood(), fireParameterChanged(), and operator=().

nbDistinctSites_

size_t bpp::TwoTreeLikelihood::nbDistinctSites_

private

Definition at line 99 of file DistanceEstimation.h.

Referenced by computeTreeD2Likelihood(), computeTreeDLikelihood(), computeTreeLikelihood(), getLikelihood(), getLogLikelihood(), and operator=().

nbSites_

size_t bpp::TwoTreeLikelihood::nbSites_

private

Definition at line 99 of file DistanceEstimation.h.

Referenced by operator=().

nbStates_

size_t bpp::TwoTreeLikelihood::nbStates_

private

Definition at line 99 of file DistanceEstimation.h.

Referenced by computeTreeD2Likelihood(), computeTreeDLikelihood(), computeTreeLikelihood(), fireParameterChanged(), and operator=().

pxy_

VVVdouble bpp::TwoTreeLikelihood::pxy_

mutableprivate

Definition at line 74 of file DistanceEstimation.h.

Referenced by computeTreeLikelihood(), fireParameterChanged(), getTransitionProbabilitiesPerRateClass(), and operator=().

rateDistribution_

DiscreteDistribution* bpp::AbstractDiscreteRatesAcrossSitesTreeLikelihood::rateDistribution_

protectedinherited

Definition at line 61 of file AbstractDiscreteRatesAcrossSitesTreeLikelihood.h.

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

rootLikelihoods_

VVVdouble bpp::TwoTreeLikelihood::rootLikelihoods_

mutableprivate

Definition at line 104 of file DistanceEstimation.h.

Referenced by computeTreeLikelihood(), getLikelihoodForASiteForARateClassForAState(), getLogLikelihoodForASiteForARateClassForAState(), and operator=().

rootLikelihoodsS_

VVdouble bpp::TwoTreeLikelihood::rootLikelihoodsS_

mutableprivate

Definition at line 105 of file DistanceEstimation.h.

Referenced by computeTreeLikelihood(), getLikelihoodForASiteForARateClass(), getLogLikelihoodForASiteForARateClass(), and operator=().

rootLikelihoodsSR_

Vdouble bpp::TwoTreeLikelihood::rootLikelihoodsSR_

mutableprivate

Definition at line 106 of file DistanceEstimation.h.

Referenced by computeTreeD2Likelihood(), computeTreeDLikelihood(), computeTreeLikelihood(), getLikelihood(), getLikelihoodForASite(), getLogLikelihood(), getLogLikelihoodForASite(), and operator=().

rootPatternLinks_

std::vector<size_t> bpp::TwoTreeLikelihood::rootPatternLinks_

private

As previous, but for the global container.

The size of this vector is equal to the number of sites in the container, each element corresponds to a site in the container and points to the corresponding column in the likelihood array of the root node. If the container contains no repeated site, there will be a strict equivalence between each site and the likelihood array of the root node. However, if this is not the case, some pointers may point toward the same element in the likelihood array.

Definition at line 91 of file DistanceEstimation.h.

Referenced by getLikelihoodForASite(), getLikelihoodForASiteForARateClass(), getLikelihoodForASiteForARateClassForAState(), getLogLikelihoodForASite(), getLogLikelihoodForASiteForARateClass(), getLogLikelihoodForASiteForARateClassForAState(), getSiteIndex(), and operator=().

rootWeights_

std::vector<unsigned int> bpp::TwoTreeLikelihood::rootWeights_

private

The frequency of each site.

Definition at line 96 of file DistanceEstimation.h.

Referenced by getLikelihood(), getLogLikelihood(), and operator=().

seqnames_

std::vector<std::string> bpp::TwoTreeLikelihood::seqnames_

private

Definition at line 70 of file DistanceEstimation.h.

Referenced by operator=().

shrunkData_

SiteContainer* bpp::TwoTreeLikelihood::shrunkData_

private

Definition at line 69 of file DistanceEstimation.h.

Referenced by operator=(), and ~TwoTreeLikelihood().

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/Distance/DistanceEstimation.h
• Bpp/Phyl/Distance/DistanceEstimation.cpp