This class implement the 'traditional' way of computing likelihood for a tree. More...

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

Inheritance diagram for bpp::RHomogeneousTreeLikelihood:

Collaboration diagram for bpp::RHomogeneousTreeLikelihood:

Public Member Functions
	RHomogeneousTreeLikelihood (const Tree &tree, SubstitutionModel model, DiscreteDistribution rDist, bool checkRooted=true, bool verbose=true, bool usePatterns=true) throw (Exception)
	Build a new RHomogeneousTreeLikelihood object without data.
	RHomogeneousTreeLikelihood (const Tree &tree, const SiteContainer &data, SubstitutionModel model, DiscreteDistribution rDist, bool checkRooted=true, bool verbose=true, bool usePatterns=true) throw (Exception)
	Build a new RHomogeneousTreeLikelihood object with data.
	RHomogeneousTreeLikelihood (const RHomogeneousTreeLikelihood &lik)
RHomogeneousTreeLikelihood &	operator= (const RHomogeneousTreeLikelihood &lik)
virtual	~RHomogeneousTreeLikelihood ()
RHomogeneousTreeLikelihood *	clone () const
void	setParameters (const ParameterList &parameters) throw (ParameterNotFoundException, ConstraintException)
	Implements the Function interface.
double	getValue () const throw (Exception)
size_t	getSiteIndex (size_t site) const throw (IndexOutOfBoundsException)
	Get the index (used for inner computations) of a given site (original alignment column).
DRASRTreeLikelihoodData *	getLikelihoodData ()
const DRASRTreeLikelihoodData *	getLikelihoodData () const
void	computeTreeLikelihood ()
virtual double	getDLikelihoodForASiteForARateClass (size_t site, size_t rateClass) const
virtual double	getDLikelihoodForASite (size_t site) const
virtual double	getDLogLikelihoodForASite (size_t site) const
virtual double	getDLogLikelihood () const
virtual void	computeTreeDLikelihood (const std::string &variable)
virtual double	getD2LikelihoodForASiteForARateClass (size_t site, size_t rateClass) const
virtual double	getD2LikelihoodForASite (size_t site) const
virtual double	getD2LogLikelihoodForASite (size_t site) const
virtual double	getD2LogLikelihood () const
virtual void	computeTreeD2Likelihood (const std::string &variable)
const SubstitutionModel *	getSubstitutionModel (int nodeId, size_t siteIndex) const throw (NodeNotFoundException)
	Get the substitution model associated to a given node and alignment column.
SubstitutionModel *	getSubstitutionModel (int nodeId, size_t siteIndex) throw (NodeNotFoundException)
	Get the substitution model associated to a given node and alignment column.
virtual void	initParameters ()
	This builds the parameters list from all parametrizable objects, i.e. substitution model, rate distribution and tree.
virtual void	applyParameters () throw (Exception)
	All parameters are stored in a parameter list. This function apply these parameters to the substitution model, to the rate distribution and to the branch lengths.
virtual void	initBranchLengthsParameters ()
virtual void	setMinimumBranchLength (double minimum) throw (Exception)
virtual void	setMaximumBranchLength (double maximum) throw (Exception)
virtual double	getMinimumBranchLength () const
virtual double	getMaximumBranchLength () const
virtual const SiteContainer *	getData () const =0
	Get the dataset for which the likelihood must be evaluated.
virtual bool	isInitialized () const =0
virtual double	getLikelihoodForASiteForAState (size_t site, int state) const =0
	Get the likelihood for a site and for a state.
virtual double	getLogLikelihoodForASiteForAState (size_t site, int state) const =0
	Get the logarithm of the likelihood for a site and for a state.
virtual Vdouble	getLikelihoodForEachSite () const =0
	Get the likelihood for each site.
virtual Vdouble	getLogLikelihoodForEachSite () const =0
	Get the logarithm of the likelihood for each site.
virtual VVdouble	getLikelihoodForEachSiteForEachState () const =0
	Get the likelihood for each site and for each state.
virtual VVdouble	getLogLikelihoodForEachSiteForEachState () const =0
	Get the logarithm of the likelihood for each site and for each state.
virtual const Tree &	getTree () const =0
	Get the tree (topology and branch lengths).
virtual size_t	getNumberOfSites () const =0
	Get the number of sites in the dataset.
virtual size_t	getNumberOfStates () const =0
	Get the number of states in the alphabet associated to the dataset.
virtual const Alphabet *	getAlphabet () const =0
	Get the alphabet associated to the dataset.
virtual void	enableDerivatives (bool yn)=0
	Tell if derivatives must be computed.
virtual ParameterList	getDerivableParameters () const =0
	All derivable parameters.
virtual ParameterList	getNonDerivableParameters () const =0
	All non derivable parameters.
virtual void	enableSecondOrderDerivatives (bool yn)=0
virtual bool	enableSecondOrderDerivatives () const =0
virtual double	d2f (const std::string &variable, const ParameterList &parameters)
virtual double	d2f (const std::string &variable1, const std::string &variable2, const ParameterList &parameters)
virtual void	enableFirstOrderDerivatives (bool yn)=0
virtual bool	enableFirstOrderDerivatives () const =0
virtual double	df (const std::string &variable, const ParameterList &parameters)
virtual double	f (const ParameterList &parameters)
virtual bool	hasParameter (const std::string &name) const =0
bool	hasParameter (const std::string &name) const
virtual const ParameterList &	getParameters () const =0
const ParameterList &	getParameters () const
virtual const Parameter &	getParameter (const std::string &name) const =0
const Parameter &	getParameter (const std::string &name) const
virtual double	getParameterValue (const std::string &name) const =0
double	getParameterValue (const std::string &name) const
virtual void	setAllParametersValues (const ParameterList &parameters)=0
void	setAllParametersValues (const ParameterList &parameters)
virtual void	setParameterValue (const std::string &name, double value)=0
void	setParameterValue (const std::string &name, double value)
virtual void	setParametersValues (const ParameterList &parameters)=0
void	setParametersValues (const ParameterList &parameters)
virtual bool	matchParametersValues (const ParameterList &parameters)=0
bool	matchParametersValues (const ParameterList &parameters)
virtual size_t	getNumberOfParameters () const =0
size_t	getNumberOfParameters () const
virtual void	setNamespace (const std::string &prefix)=0
void	setNamespace (const std::string &prefix)
virtual std::string	getNamespace () const =0
std::string	getNamespace () const
virtual std::string	getParameterNameWithoutNamespace (const std::string &name) const =0
std::string	getParameterNameWithoutNamespace (const std::string &name) const
The TreeLikelihood interface.
Other methods are implemented in the AbstractHomogeneousTreeLikelihood class.
void	setData (const SiteContainer &sites) throw (Exception)
	Set the dataset for which the likelihood must be evaluated.
double	getLikelihood () const
	Get the likelihood for the whole dataset.
double	getLogLikelihood () const
	Get the logarithm of the likelihood for the whole dataset.
double	getLikelihoodForASite (size_t site) const
	Get the likelihood for a site.
double	getLogLikelihoodForASite (size_t site) const
	Get the logarithm of the likelihood for a site.
The DiscreteRatesAcrossSites interface implementation:
double	getLikelihoodForASiteForARateClass (size_t site, size_t rateClass) const
	Get the likelihood for a site knowing its rate class.
double	getLogLikelihoodForASiteForARateClass (size_t site, size_t rateClass) const
	Get the logarithm of the likelihood for a site knowing its rate class.
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.
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.
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.
void	initialize () throw (Exception)
	Init the likelihood object.
ParameterList	getBranchLengthsParameters () const
	Get the branch lengths parameters.
ParameterList	getSubstitutionModelParameters () const
	Get the parameters associated to substitution model(s).
ParameterList	getRateDistributionParameters () const
	Get the parameters associated to the rate distirbution.
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.
VVVdouble	getTransitionProbabilitiesPerRateClass (int nodeId, size_t siteIndex) const
	Retrieves all Pij(t) for a particular branch, defined by the upper node.
ConstBranchModelIterator *	getNewBranchModelIterator (int nodeId) const
ConstSiteModelIterator *	getNewSiteModelIterator (size_t siteIndex) const
The HomogeneousTreeLikelihood interface.
Other methods are implemented in the AbstractTreeLikelihood class.
const SubstitutionModel *	getSubstitutionModel () const
SubstitutionModel *	getSubstitutionModel ()
void	setSubstitutionModel (SubstitutionModel *model) throw (Exception)
The TreeLikelihood interface.
const SiteContainer *	getData () const
	Get the dataset for which the likelihood must be evaluated.
bool	isInitialized () const
Vdouble	getLikelihoodForEachSite () const
	Get the likelihood for each site.
Vdouble	getLogLikelihoodForEachSite () const
	Get the logarithm of the likelihood for each site.
VVdouble	getLikelihoodForEachSiteForEachState () const
	Get the likelihood for each site and for each state.
VVdouble	getLogLikelihoodForEachSiteForEachState () const
	Get the logarithm of the likelihood for each site and for each state.
const Tree &	getTree () const
	Get the tree (topology and branch lengths).
size_t	getNumberOfSites () const
	Get the number of sites in the dataset.
size_t	getNumberOfStates () const
	Get the number of states in the alphabet associated to the dataset.
const Alphabet *	getAlphabet () const
	Get the alphabet associated to the dataset.
void	enableDerivatives (bool yn)
	Tell if derivatives must be computed.
void	enableSecondOrderDerivatives (bool yn)
bool	enableSecondOrderDerivatives () const
void	enableFirstOrderDerivatives (bool yn)
bool	enableFirstOrderDerivatives () const
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.
double	getLogLikelihoodForASiteForAState (size_t site, int state) const
	Get the logarithm of the likelihood for a site and for a state.
VVdouble	getTransitionProbabilities (int nodeId, size_t siteIndex) const
	Retrieves all Pij(t) for a particular branch, defined by the upper node and site.
ParameterList	getDerivableParameters () const
	All derivable parameters.
ParameterList	getNonDerivableParameters () const
	All non derivable parameters.
Retrieve some particular parameters subsets.
virtual VVdouble	getTransitionProbabilities (int nodeId, size_t siteIndex) const =0
	Retrieves all Pij(t) for a particular branch, defined by the upper node and site.
The DiscreteRatesAcrossSites interface implementation:
const DiscreteDistribution *	getRateDistribution () const
	Get the rate distribution used for the computation.
DiscreteDistribution *	getRateDistribution ()
	Get the rate distribution used for the computation.
size_t	getNumberOfClasses () const
	Get the number of classes.
VVdouble	getLikelihoodForEachSiteForEachRateClass () const
	Get the likelihood for each site and each rate class.
VVdouble	getLogLikelihoodForEachSiteForEachRateClass () const
	Get the logarithm of the likelihood for each site and each rate class.
VVVdouble	getLikelihoodForEachSiteForEachRateClassForEachState () const
	Get the likelihood for each site and each rate class and each state.
VVVdouble	getLogLikelihoodForEachSiteForEachRateClassForEachState () const
	Get the logarithm of the likelihood for each site and each rate class and each state.
VVdouble	getPosteriorProbabilitiesOfEachRate () const
	Get the posterior probability for each site of belonging to a particular rate class.
Vdouble	getRateWithMaxPostProbOfEachSite () const
	Get the posterior rate (the one with maximum posterior probability) for each site.
std::vector< size_t >	getRateClassWithMaxPostProbOfEachSite () const
	Get the posterior rate class (the one with maximum posterior probability) for each site.
Vdouble	getPosteriorRateOfEachSite () const
	Get the posterior rate, i.e. averaged over all classes and weighted with posterior probabilities, for each site.
Static Public Member Functions
Generic tools to deal with likelihood arrays
static void	resetLikelihoodArray (VVVdouble &likelihoodArray)
	Set all conditional likelihoods to 1.
static void	displayLikelihoodArray (const VVVdouble &likelihoodArray)
	Print the likelihood array to terminal (debugging tool).
Protected Member Functions
virtual void	computeSubtreeLikelihood (const Node *node)
	Compute the likelihood for a subtree defined by the Tree::Node node.
virtual void	computeDownSubtreeDLikelihood (const Node *)
virtual void	computeDownSubtreeD2Likelihood (const Node *)
void	fireParameterChanged (const ParameterList &params)
virtual void	displayLikelihood (const Node *node)
	This method is mainly for debugging purpose.
virtual void	computeAllTransitionProbabilities ()
	Fill the pxy_, dpxy_ and d2pxy_ arrays for all nodes.
virtual void	computeTransitionProbabilitiesForNode (const Node *node)
	Fill the pxy_, dpxy_ and d2pxy_ arrays for one node.
void	addParameter_ (Parameter *parameter)
void	addParameters_ (const ParameterList &parameters)
void	deleteParameter_ (size_t index)
void	resetParameters_ ()
Parameter &	getParameter_ (const std::string &name)
Parameter &	getParameter_ (size_t index)
const Parameter &	getParameter_ (size_t index) const
Parameter &	getParameterWithNamespace_ (const std::string &name)
const Parameter &	getParameterWithNamespace_ (const std::string &name) const
ParameterList &	getParameters_ ()
Protected Attributes
double	minusLogLik_
SubstitutionModel *	model_
ParameterList	brLenParameters_
std::map< int, VVVdouble >	pxy_
std::map< int, VVVdouble >	dpxy_
std::map< int, VVVdouble >	d2pxy_
std::vector< double >	rootFreqs_
std::vector< Node * >	nodes_
	Pointer toward all nodes in the tree.
size_t	nbSites_
size_t	nbDistinctSites_
size_t	nbClasses_
size_t	nbStates_
size_t	nbNodes_
bool	verbose_
double	minimumBrLen_
double	maximumBrLen_
std::auto_ptr< Constraint >	brLenConstraint_
DiscreteDistribution *	rateDistribution_
const SiteContainer *	data_
TreeTemplate< Node > *	tree_
bool	computeFirstOrderDerivatives_
bool	computeSecondOrderDerivatives_
bool	initialized_
Private Member Functions
void	init_ (bool usePatterns) throw (Exception)
	Method called by constructors.
Private Attributes
DRASRTreeLikelihoodData *	likelihoodData_
Friends
class	RHomogeneousMixedTreeLikelihood

Detailed Description

This class implement the 'traditional' way of computing likelihood for a tree.

The substitution model is constant over the tree (homogeneous model). A non uniform distribution of rates among the sites is allowed (ASRV models).

This class uses an instance of the DRASRTreeLikelihoodData for conditionnal likelihood storage.

This class can also use a simple or recursive site compression. In the simple case, computations for identical sites are not duplicated. In the recursive case, computations for identical sub-sites (site patterns ) are also not duplicated: Following N. Galtier (personal communication ;-), we define a Pattern as a distinct site in a sub-dataset corresponding to the dataset with sequences associated to a particular subtree. The likelihood computation is the same for a given site, hence the idea is to save time from performing many times the same coputation. The network between all patterns is defined by the _patternLinks double map, initialized in the initLikelihoodsWithPatterns() method. This initialisation takes more time than the classic initTreeLikelihood one, where all likelihoods for a given site i are at the i coordinate in the likelihood tensor, but is really faster when computing the likelihood (computeLikelihoods() method). Hence, if you have to compute likelihood many times while holding the tree topology unchanged, you should use patterns. This decreases the likelihood computation time, but at a cost: some time is spent to establish the patterns relationships. Whether to use or not patterns depends on what you actllay need:

The more you compute likelihoods without changing the data or topology, the more patterns are interesting (this divides the cost of computing patterns by the number of computation performed). Patterns are hence usefull when you have a high number of computation to perform, while optimizing numerical parameters for instance).
Patterns are more likely to occur whith small alphabet (nucleotides).

Definition at line 82 of file RHomogeneousTreeLikelihood.h.

Constructor & Destructor Documentation

RHomogeneousTreeLikelihood::RHomogeneousTreeLikelihood	(	const Tree &	tree,
		SubstitutionModel *	model,
		DiscreteDistribution *	rDist,
		bool	checkRooted = `true`,
		bool	verbose = `true`,
		bool	usePatterns = `true`
	)		throw (Exception)

Build a new RHomogeneousTreeLikelihood object without data.

This constructor only initialize the parameters. To compute a likelihood, you will need to call the setData() and the computeTreeLikelihood() methods.

Parameters:

tree	The tree to use.
model	The substitution model to use.
rDist	The rate across sites distribution to use.
checkRooted	Tell if we have to check for the tree to be unrooted. If true, any rooted tree will be unrooted before likelihood computation.
verbose	Should I display some info?
usePatterns	Tell if recursive site compression should be performed.

Exceptions:

Exception in an error occured.

Definition at line 55 of file RHomogeneousTreeLikelihood.cpp.

Referenced by clone().

RHomogeneousTreeLikelihood::RHomogeneousTreeLikelihood	(	const Tree &	tree,
		const SiteContainer &	data,
		SubstitutionModel *	model,
		DiscreteDistribution *	rDist,
		bool	checkRooted = `true`,
		bool	verbose = `true`,
		bool	usePatterns = `true`
	)		throw (Exception)

Build a new RHomogeneousTreeLikelihood object with data.

This constructor initializes all parameters, data, and likelihood arrays.

Parameters:

tree	The tree to use.
data	Sequences to use.
model	The substitution model to use.
rDist	The rate across sites distribution to use.
checkRooted	Tell if we have to check for the tree to be unrooted. If true, any rooted tree will be unrooted before likelihood computation.
verbose	Should I display some info?
usePatterns	Tell if recursive site compression should be performed.

Exceptions:

Exception in an error occured.

Definition at line 72 of file RHomogeneousTreeLikelihood.cpp.

RHomogeneousTreeLikelihood::RHomogeneousTreeLikelihood ( const RHomogeneousTreeLikelihood & lik )

Definition at line 101 of file RHomogeneousTreeLikelihood.cpp.

References bpp::DRASRTreeLikelihoodData::clone(), likelihoodData_, bpp::DRASRTreeLikelihoodData::setTree(), and bpp::AbstractTreeLikelihood::tree_.

RHomogeneousTreeLikelihood::~RHomogeneousTreeLikelihood ( ) [virtual]

Definition at line 126 of file RHomogeneousTreeLikelihood.cpp.

References likelihoodData_.

Member Function Documentation

void AbstractHomogeneousTreeLikelihood::applyParameters ( ) throw (Exception) [virtual, inherited]

All parameters are stored in a parameter list. This function apply these parameters to the substitution model, to the rate distribution and to the branch lengths.

Reimplemented in bpp::RHomogeneousClockTreeLikelihood.

Definition at line 286 of file AbstractHomogeneousTreeLikelihood.cpp.

References bpp::SubstitutionModel::getFrequencies(), bpp::AbstractParametrizable::getParameter(), bpp::AbstractParametrizable::getParameters(), bpp::Parameter::getValue(), bpp::AbstractTreeLikelihood::initialized_, bpp::ParameterAliasable::matchParametersValues(), bpp::DiscreteDistribution::matchParametersValues(), bpp::AbstractHomogeneousTreeLikelihood::model_, bpp::AbstractHomogeneousTreeLikelihood::nbNodes_, bpp::AbstractHomogeneousTreeLikelihood::nodes_, bpp::AbstractDiscreteRatesAcrossSitesTreeLikelihood::rateDistribution_, bpp::AbstractHomogeneousTreeLikelihood::rootFreqs_, and bpp::TextTools::toString().

Referenced by bpp::RHomogeneousMixedTreeLikelihood::fireParameterChanged(), bpp::DRHomogeneousMixedTreeLikelihood::fireParameterChanged(), bpp::DRHomogeneousTreeLikelihood::fireParameterChanged(), and fireParameterChanged().

RHomogeneousTreeLikelihood* bpp::RHomogeneousTreeLikelihood::clone ( ) const [inline, virtual]

Implements bpp::HomogeneousTreeLikelihood.

Reimplemented in bpp::RHomogeneousMixedTreeLikelihood, and bpp::RHomogeneousClockTreeLikelihood.

Definition at line 148 of file RHomogeneousTreeLikelihood.h.

References RHomogeneousTreeLikelihood().

void AbstractHomogeneousTreeLikelihood::computeAllTransitionProbabilities ( ) [protected, virtual, inherited]

Fill the pxy_, dpxy_ and d2pxy_ arrays for all nodes.

Reimplemented in bpp::RHomogeneousMixedTreeLikelihood.

Definition at line 340 of file AbstractHomogeneousTreeLikelihood.cpp.

References bpp::AbstractHomogeneousTreeLikelihood::computeTransitionProbabilitiesForNode(), bpp::SubstitutionModel::getFrequencies(), bpp::AbstractHomogeneousTreeLikelihood::model_, bpp::AbstractHomogeneousTreeLikelihood::nbNodes_, bpp::AbstractHomogeneousTreeLikelihood::nodes_, and bpp::AbstractHomogeneousTreeLikelihood::rootFreqs_.

Referenced by bpp::DRHomogeneousTreeLikelihood::fireParameterChanged(), and fireParameterChanged().

void RHomogeneousTreeLikelihood::computeDownSubtreeD2Likelihood ( const Node * node ) [protected, virtual]

Reimplemented in bpp::RHomogeneousMixedTreeLikelihood.

Definition at line 711 of file RHomogeneousTreeLikelihood.cpp.

References bpp::DRASRTreeLikelihoodData::getArrayPositions(), bpp::DRASRTreeLikelihoodData::getD2LikelihoodArray(), bpp::Node::getFather(), bpp::Node::getId(), bpp::DRASRTreeLikelihoodData::getLikelihoodArray(), bpp::Node::getNumberOfSons(), bpp::Node::getSon(), likelihoodData_, bpp::AbstractHomogeneousTreeLikelihood::nbClasses_, bpp::AbstractHomogeneousTreeLikelihood::nbStates_, and bpp::AbstractHomogeneousTreeLikelihood::pxy_.

Referenced by computeTreeD2Likelihood().

void RHomogeneousTreeLikelihood::computeDownSubtreeDLikelihood ( const Node * node ) [protected, virtual]

Reimplemented in bpp::RHomogeneousMixedTreeLikelihood.

Definition at line 460 of file RHomogeneousTreeLikelihood.cpp.

References bpp::DRASRTreeLikelihoodData::getArrayPositions(), bpp::DRASRTreeLikelihoodData::getDLikelihoodArray(), bpp::Node::getFather(), bpp::Node::getId(), bpp::DRASRTreeLikelihoodData::getLikelihoodArray(), bpp::Node::getNumberOfSons(), bpp::Node::getSon(), likelihoodData_, bpp::AbstractHomogeneousTreeLikelihood::nbClasses_, bpp::AbstractHomogeneousTreeLikelihood::nbStates_, and bpp::AbstractHomogeneousTreeLikelihood::pxy_.

Referenced by computeTreeDLikelihood().

void RHomogeneousTreeLikelihood::computeSubtreeLikelihood ( const Node * node ) [protected, virtual]

Compute the likelihood for a subtree defined by the Tree::Node node.

Parameters:

node	The root of the subtree.

Reimplemented in bpp::RHomogeneousMixedTreeLikelihood.

Definition at line 808 of file RHomogeneousTreeLikelihood.cpp.

References bpp::DRASRTreeLikelihoodData::getArrayPositions(), bpp::Node::getId(), bpp::DRASRTreeLikelihoodData::getLikelihoodArray(), bpp::Node::getNumberOfSons(), bpp::Node::getSon(), bpp::Node::isLeaf(), likelihoodData_, bpp::AbstractHomogeneousTreeLikelihood::nbClasses_, bpp::AbstractHomogeneousTreeLikelihood::nbStates_, and bpp::AbstractHomogeneousTreeLikelihood::pxy_.

Referenced by computeTreeLikelihood().

void AbstractHomogeneousTreeLikelihood::computeTransitionProbabilitiesForNode ( const Node * node ) [protected, virtual, inherited]

Fill the pxy_, dpxy_ and d2pxy_ arrays for one node.

Reimplemented in bpp::RHomogeneousMixedTreeLikelihood.

Definition at line 353 of file AbstractHomogeneousTreeLikelihood.cpp.

References bpp::AbstractTreeLikelihood::computeFirstOrderDerivatives_, bpp::AbstractTreeLikelihood::computeSecondOrderDerivatives_, bpp::AbstractHomogeneousTreeLikelihood::d2pxy_, bpp::AbstractHomogeneousTreeLikelihood::dpxy_, bpp::DiscreteDistribution::getCategory(), bpp::SubstitutionModel::getd2Pij_dt2(), bpp::Node::getDistanceToFather(), bpp::SubstitutionModel::getdPij_dt(), bpp::Node::getId(), bpp::SubstitutionModel::getPij_t(), bpp::AbstractHomogeneousTreeLikelihood::model_, bpp::AbstractHomogeneousTreeLikelihood::nbClasses_, bpp::AbstractHomogeneousTreeLikelihood::nbStates_, bpp::AbstractHomogeneousTreeLikelihood::pxy_, and bpp::AbstractDiscreteRatesAcrossSitesTreeLikelihood::rateDistribution_.

Referenced by bpp::AbstractHomogeneousTreeLikelihood::computeAllTransitionProbabilities(), bpp::DRHomogeneousTreeLikelihood::fireParameterChanged(), and fireParameterChanged().

void RHomogeneousTreeLikelihood::computeTreeD2Likelihood ( const std::string & variable ) [virtual]

Reimplemented in bpp::RHomogeneousMixedTreeLikelihood.

Definition at line 621 of file RHomogeneousTreeLikelihood.cpp.

References computeDownSubtreeD2Likelihood(), bpp::AbstractHomogeneousTreeLikelihood::d2pxy_, bpp::DRASRTreeLikelihoodData::getArrayPositions(), bpp::DRASRTreeLikelihoodData::getD2LikelihoodArray(), bpp::Node::getFather(), bpp::Node::getId(), bpp::DRASRTreeLikelihoodData::getLikelihoodArray(), bpp::Node::getNumberOfSons(), bpp::Node::getSon(), likelihoodData_, bpp::AbstractHomogeneousTreeLikelihood::nbClasses_, bpp::AbstractHomogeneousTreeLikelihood::nbStates_, bpp::AbstractHomogeneousTreeLikelihood::nodes_, and bpp::AbstractHomogeneousTreeLikelihood::pxy_.

void RHomogeneousTreeLikelihood::computeTreeDLikelihood ( const std::string & variable ) [virtual]

Reimplemented in bpp::RHomogeneousMixedTreeLikelihood.

Definition at line 370 of file RHomogeneousTreeLikelihood.cpp.

References computeDownSubtreeDLikelihood(), bpp::AbstractHomogeneousTreeLikelihood::dpxy_, bpp::DRASRTreeLikelihoodData::getArrayPositions(), bpp::DRASRTreeLikelihoodData::getDLikelihoodArray(), bpp::Node::getFather(), bpp::Node::getId(), bpp::DRASRTreeLikelihoodData::getLikelihoodArray(), bpp::Node::getNumberOfSons(), bpp::Node::getSon(), likelihoodData_, bpp::AbstractHomogeneousTreeLikelihood::nbClasses_, bpp::AbstractHomogeneousTreeLikelihood::nbStates_, bpp::AbstractHomogeneousTreeLikelihood::nodes_, and bpp::AbstractHomogeneousTreeLikelihood::pxy_.

void RHomogeneousTreeLikelihood::computeTreeLikelihood ( )

Reimplemented in bpp::RHomogeneousMixedTreeLikelihood.

Definition at line 801 of file RHomogeneousTreeLikelihood.cpp.

References computeSubtreeLikelihood(), bpp::TreeTemplate< N >::getRootNode(), and bpp::AbstractTreeLikelihood::tree_.

Referenced by fireParameterChanged().

void RHomogeneousTreeLikelihood::displayLikelihood ( const Node * node ) [protected, virtual]

This method is mainly for debugging purpose.

Parameters:

node	The node at which likelihood values must be displayed.

Reimplemented in bpp::RHomogeneousMixedTreeLikelihood.

Definition at line 874 of file RHomogeneousTreeLikelihood.cpp.

References bpp::AbstractDiscreteRatesAcrossSitesTreeLikelihood::displayLikelihoodArray(), bpp::Node::getId(), bpp::DRASRTreeLikelihoodData::getLikelihoodArray(), bpp::Node::getName(), and likelihoodData_.

void AbstractDiscreteRatesAcrossSitesTreeLikelihood::displayLikelihoodArray ( const VVVdouble & likelihoodArray ) [static, inherited]

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(), displayLikelihood(), and bpp::RNonHomogeneousTreeLikelihood::displayLikelihood().

void bpp::AbstractTreeLikelihood::enableDerivatives ( bool yn ) [inline, virtual, inherited]

Tell if derivatives must be computed.

This methods calls the enableFirstOrderDerivatives and enableSecondOrderDerivatives.

Parameters:

yn	Yes or no.

Implements bpp::TreeLikelihood.

Definition at line 293 of file AbstractTreeLikelihood.h.

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

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

virtual void bpp::TreeLikelihood::enableDerivatives ( bool yn ) [pure virtual, inherited]

Tell if derivatives must be computed.

This methods calls the enableFirstOrderDerivatives and enableSecondOrderDerivatives.

Parameters:

yn	Yes or no.

Implemented in bpp::AbstractTreeLikelihood.

void bpp::AbstractTreeLikelihood::enableFirstOrderDerivatives ( bool yn ) [inline, virtual, inherited]

Implements bpp::DerivableSecondOrder.

Definition at line 294 of file AbstractTreeLikelihood.h.

References bpp::AbstractTreeLikelihood::computeFirstOrderDerivatives_.

bool bpp::AbstractTreeLikelihood::enableFirstOrderDerivatives ( ) const [inline, virtual, inherited]

Implements bpp::DerivableSecondOrder.

Definition at line 296 of file AbstractTreeLikelihood.h.

References bpp::AbstractTreeLikelihood::computeFirstOrderDerivatives_.

void bpp::AbstractTreeLikelihood::enableSecondOrderDerivatives ( bool yn ) [inline, virtual, inherited]

Implements bpp::DerivableSecondOrder.

Definition at line 295 of file AbstractTreeLikelihood.h.

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

bool bpp::AbstractTreeLikelihood::enableSecondOrderDerivatives ( ) const [inline, virtual, inherited]

Implements bpp::DerivableSecondOrder.

Definition at line 297 of file AbstractTreeLikelihood.h.

References bpp::AbstractTreeLikelihood::computeSecondOrderDerivatives_.

void RHomogeneousTreeLikelihood::fireParameterChanged ( const ParameterList & params ) [protected, virtual]

Implements bpp::AbstractParametrizable.

Reimplemented in bpp::RHomogeneousMixedTreeLikelihood, and bpp::RHomogeneousClockTreeLikelihood.

Definition at line 258 of file RHomogeneousTreeLikelihood.cpp.

References bpp::AbstractHomogeneousTreeLikelihood::applyParameters(), bpp::AbstractHomogeneousTreeLikelihood::computeAllTransitionProbabilities(), bpp::AbstractHomogeneousTreeLikelihood::computeTransitionProbabilitiesForNode(), computeTreeLikelihood(), bpp::ParameterList::getCommonParametersWith(), bpp::SubstitutionModel::getFrequencies(), getLogLikelihood(), bpp::ParameterAliasable::getParameters(), bpp::DiscreteDistribution::getParameters(), minusLogLik_, bpp::AbstractHomogeneousTreeLikelihood::model_, bpp::AbstractHomogeneousTreeLikelihood::nodes_, bpp::AbstractDiscreteRatesAcrossSitesTreeLikelihood::rateDistribution_, bpp::AbstractHomogeneousTreeLikelihood::rootFreqs_, and bpp::ParameterList::size().

const Alphabet* bpp::AbstractTreeLikelihood::getAlphabet ( ) const [inline, virtual, inherited]

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_, and bpp::SiteContainer::getAlphabet().

virtual const Alphabet* bpp::TreeLikelihood::getAlphabet ( ) const [pure virtual, inherited]

Get the alphabet associated to the dataset.

Returns:: the alphabet associated to the dataset.

Implemented in bpp::AbstractTreeLikelihood.

ParameterList AbstractHomogeneousTreeLikelihood::getBranchLengthsParameters ( ) const [virtual, inherited]

Get the branch lengths parameters.

Returns:: A ParameterList with all branch lengths.

Implements bpp::TreeLikelihood.

Definition at line 250 of file AbstractHomogeneousTreeLikelihood.cpp.

References bpp::AbstractHomogeneousTreeLikelihood::brLenParameters_, bpp::ParameterList::getCommonParametersWith(), bpp::AbstractParametrizable::getParameters(), and bpp::AbstractTreeLikelihood::initialized_.

double RHomogeneousTreeLikelihood::getD2LikelihoodForASite ( size_t site ) const [virtual]

Definition at line 567 of file RHomogeneousTreeLikelihood.cpp.

References getD2LikelihoodForASiteForARateClass(), bpp::DiscreteDistribution::getProbability(), bpp::AbstractHomogeneousTreeLikelihood::nbClasses_, and bpp::AbstractDiscreteRatesAcrossSitesTreeLikelihood::rateDistribution_.

Referenced by getD2LogLikelihoodForASite().

double RHomogeneousTreeLikelihood::getD2LikelihoodForASiteForARateClass	(	size_t	site,
		size_t	rateClass
	)		const `[virtual]`

Reimplemented in bpp::RHomogeneousMixedTreeLikelihood.

Definition at line 552 of file RHomogeneousTreeLikelihood.cpp.

References bpp::DRASRTreeLikelihoodData::getD2LikelihoodArray(), bpp::Node::getId(), bpp::DRASRTreeLikelihoodData::getRootArrayPosition(), bpp::TreeTemplate< N >::getRootNode(), likelihoodData_, bpp::AbstractHomogeneousTreeLikelihood::nbStates_, bpp::AbstractHomogeneousTreeLikelihood::rootFreqs_, and bpp::AbstractTreeLikelihood::tree_.

Referenced by getD2LikelihoodForASite().

double RHomogeneousTreeLikelihood::getD2LogLikelihood ( ) const [virtual]

Definition at line 588 of file RHomogeneousTreeLikelihood.cpp.

References getD2LogLikelihoodForASite(), and bpp::AbstractHomogeneousTreeLikelihood::nbSites_.

double RHomogeneousTreeLikelihood::getD2LogLikelihoodForASite ( size_t site ) const [virtual]

Definition at line 580 of file RHomogeneousTreeLikelihood.cpp.

References getD2LikelihoodForASite(), getDLikelihoodForASite(), and getLikelihoodForASite().

Referenced by getD2LogLikelihood().

virtual const SiteContainer* bpp::TreeLikelihood::getData ( ) const [pure virtual, inherited]

Get the dataset for which the likelihood must be evaluated.

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

Implemented in bpp::AbstractTreeLikelihood.

const SiteContainer* bpp::AbstractTreeLikelihood::getData ( ) const [inline, virtual, inherited]

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().

ParameterList AbstractDiscreteRatesAcrossSitesTreeLikelihood::getDerivableParameters ( ) const [virtual, inherited]

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.

virtual ParameterList bpp::TreeLikelihood::getDerivableParameters ( ) const [pure virtual, inherited]

All derivable parameters.

Usually, this contains all branch lengths parameters.

Returns:: A ParameterList.

Implemented in bpp::RHomogeneousClockTreeLikelihood, and bpp::AbstractDiscreteRatesAcrossSitesTreeLikelihood.

double RHomogeneousTreeLikelihood::getDLikelihoodForASite ( size_t site ) const [virtual]

Definition at line 316 of file RHomogeneousTreeLikelihood.cpp.

References getDLikelihoodForASiteForARateClass(), bpp::DiscreteDistribution::getProbability(), bpp::AbstractHomogeneousTreeLikelihood::nbClasses_, and bpp::AbstractDiscreteRatesAcrossSitesTreeLikelihood::rateDistribution_.

Referenced by getD2LogLikelihoodForASite(), and getDLogLikelihoodForASite().

double RHomogeneousTreeLikelihood::getDLikelihoodForASiteForARateClass	(	size_t	site,
		size_t	rateClass
	)		const `[virtual]`

Reimplemented in bpp::RHomogeneousMixedTreeLikelihood.

Definition at line 301 of file RHomogeneousTreeLikelihood.cpp.

References bpp::DRASRTreeLikelihoodData::getDLikelihoodArray(), bpp::Node::getId(), bpp::DRASRTreeLikelihoodData::getRootArrayPosition(), bpp::TreeTemplate< N >::getRootNode(), likelihoodData_, bpp::AbstractHomogeneousTreeLikelihood::nbStates_, bpp::AbstractHomogeneousTreeLikelihood::rootFreqs_, and bpp::AbstractTreeLikelihood::tree_.

Referenced by getDLikelihoodForASite().

double RHomogeneousTreeLikelihood::getDLogLikelihood ( ) const [virtual]

Definition at line 337 of file RHomogeneousTreeLikelihood.cpp.

References getDLogLikelihoodForASite(), and bpp::AbstractHomogeneousTreeLikelihood::nbSites_.

double RHomogeneousTreeLikelihood::getDLogLikelihoodForASite ( size_t site ) const [virtual]

Definition at line 329 of file RHomogeneousTreeLikelihood.cpp.

References getDLikelihoodForASite(), and getLikelihoodForASite().

Referenced by getDLogLikelihood().

double RHomogeneousTreeLikelihood::getFirstOrderDerivative ( const std::string & variable ) const throw (Exception) [virtual]

Implements bpp::DerivableSecondOrder.

Reimplemented in bpp::RHomogeneousClockTreeLikelihood.

Definition at line 350 of file RHomogeneousTreeLikelihood.cpp.

double RHomogeneousTreeLikelihood::getLikelihood ( ) const [virtual]

Get the likelihood for the whole dataset.

Returns:: The likelihood of the dataset.

Implements bpp::TreeLikelihood.

Definition at line 152 of file RHomogeneousTreeLikelihood.cpp.

References getLikelihoodForASite(), and bpp::AbstractHomogeneousTreeLikelihood::nbSites_.

DRASRTreeLikelihoodData* bpp::RHomogeneousTreeLikelihood::getLikelihoodData ( ) [inline, virtual]

Returns:: The underlying likelihood data structure.

Implements bpp::TreeLikelihood.

Definition at line 222 of file RHomogeneousTreeLikelihood.h.

References likelihoodData_.

const DRASRTreeLikelihoodData* bpp::RHomogeneousTreeLikelihood::getLikelihoodData ( ) const [inline, virtual]

Returns:: The underlying likelihood data structure.

Implements bpp::TreeLikelihood.

Definition at line 223 of file RHomogeneousTreeLikelihood.h.

References likelihoodData_.

double RHomogeneousTreeLikelihood::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 182 of file RHomogeneousTreeLikelihood.cpp.

References getLikelihoodForASiteForARateClass(), bpp::DiscreteDistribution::getProbability(), bpp::AbstractHomogeneousTreeLikelihood::nbClasses_, and bpp::AbstractDiscreteRatesAcrossSitesTreeLikelihood::rateDistribution_.

Referenced by getD2LogLikelihoodForASite(), getDLogLikelihoodForASite(), and getLikelihood().

double RHomogeneousTreeLikelihood::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.

Reimplemented in bpp::RHomogeneousMixedTreeLikelihood.

Definition at line 207 of file RHomogeneousTreeLikelihood.cpp.

References bpp::Node::getId(), bpp::DRASRTreeLikelihoodData::getLikelihoodArray(), bpp::DRASRTreeLikelihoodData::getRootArrayPosition(), bpp::TreeTemplate< N >::getRootNode(), likelihoodData_, bpp::AbstractHomogeneousTreeLikelihood::nbStates_, bpp::AbstractHomogeneousTreeLikelihood::rootFreqs_, and bpp::AbstractTreeLikelihood::tree_.

Referenced by getLikelihoodForASite(), and getLogLikelihoodForASite().

double RHomogeneousTreeLikelihood::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.

Reimplemented in bpp::RHomogeneousMixedTreeLikelihood.

Definition at line 236 of file RHomogeneousTreeLikelihood.cpp.

References bpp::Node::getId(), bpp::DRASRTreeLikelihoodData::getLikelihoodArray(), bpp::DRASRTreeLikelihoodData::getRootArrayPosition(), bpp::TreeTemplate< N >::getRootNode(), likelihoodData_, and bpp::AbstractTreeLikelihood::tree_.

double AbstractDiscreteRatesAcrossSitesTreeLikelihood::getLikelihoodForASiteForAState	(	size_t	site,
		int	state
	)		const `[virtual, inherited]`

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.

virtual double bpp::TreeLikelihood::getLikelihoodForASiteForAState	(	size_t	site,
		int	state
	)		const `[pure virtual, inherited]`

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.

Implemented in bpp::AbstractDiscreteRatesAcrossSitesTreeLikelihood.

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

virtual Vdouble bpp::TreeLikelihood::getLikelihoodForEachSite ( ) const [pure virtual, inherited]

Get the likelihood for each site.

Returns:: A vector with all likelihoods for each site.

Implemented in bpp::AbstractTreeLikelihood.

Vdouble AbstractTreeLikelihood::getLikelihoodForEachSite ( ) const [virtual, inherited]

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().

VVdouble AbstractDiscreteRatesAcrossSitesTreeLikelihood::getLikelihoodForEachSiteForEachRateClass ( ) const [virtual, inherited]

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.

VVVdouble AbstractDiscreteRatesAcrossSitesTreeLikelihood::getLikelihoodForEachSiteForEachRateClassForEachState ( ) const [virtual, inherited]

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.

virtual VVdouble bpp::TreeLikelihood::getLikelihoodForEachSiteForEachState ( ) const [pure virtual, inherited]

Get the likelihood for each site and for each state.

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

Implemented in bpp::AbstractTreeLikelihood.

VVdouble AbstractTreeLikelihood::getLikelihoodForEachSiteForEachState ( ) const [virtual, inherited]

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::AbstractTreeLikelihood::getNumberOfStates().

double RHomogeneousTreeLikelihood::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 164 of file RHomogeneousTreeLikelihood.cpp.

References getLogLikelihoodForASite(), and bpp::AbstractHomogeneousTreeLikelihood::nbSites_.

Referenced by bpp::RHomogeneousMixedTreeLikelihood::fireParameterChanged(), and fireParameterChanged().

double RHomogeneousTreeLikelihood::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 194 of file RHomogeneousTreeLikelihood.cpp.

References getLikelihoodForASiteForARateClass(), bpp::DiscreteDistribution::getProbability(), bpp::AbstractHomogeneousTreeLikelihood::nbClasses_, and bpp::AbstractDiscreteRatesAcrossSitesTreeLikelihood::rateDistribution_.

Referenced by getLogLikelihood().

double RHomogeneousTreeLikelihood::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.

Reimplemented in bpp::RHomogeneousMixedTreeLikelihood.

Definition at line 222 of file RHomogeneousTreeLikelihood.cpp.

References bpp::Node::getId(), bpp::DRASRTreeLikelihoodData::getLikelihoodArray(), bpp::DRASRTreeLikelihoodData::getRootArrayPosition(), bpp::TreeTemplate< N >::getRootNode(), likelihoodData_, bpp::AbstractHomogeneousTreeLikelihood::nbStates_, bpp::AbstractHomogeneousTreeLikelihood::rootFreqs_, and bpp::AbstractTreeLikelihood::tree_.

double RHomogeneousTreeLikelihood::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.

Reimplemented in bpp::RHomogeneousMixedTreeLikelihood.

Definition at line 243 of file RHomogeneousTreeLikelihood.cpp.

References bpp::Node::getId(), bpp::DRASRTreeLikelihoodData::getLikelihoodArray(), bpp::DRASRTreeLikelihoodData::getRootArrayPosition(), bpp::TreeTemplate< N >::getRootNode(), likelihoodData_, and bpp::AbstractTreeLikelihood::tree_.

double AbstractDiscreteRatesAcrossSitesTreeLikelihood::getLogLikelihoodForASiteForAState	(	size_t	site,
		int	state
	)		const `[virtual, inherited]`

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.

virtual double bpp::TreeLikelihood::getLogLikelihoodForASiteForAState	(	size_t	site,
		int	state
	)		const `[pure virtual, inherited]`

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.

Implemented in bpp::AbstractDiscreteRatesAcrossSitesTreeLikelihood.

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

virtual Vdouble bpp::TreeLikelihood::getLogLikelihoodForEachSite ( ) const [pure virtual, inherited]

Get the logarithm of the likelihood for each site.

Returns:: A vector with all log likelihoods for each site.

Implemented in bpp::AbstractTreeLikelihood.

Vdouble AbstractTreeLikelihood::getLogLikelihoodForEachSite ( ) const [virtual, inherited]

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().

VVdouble AbstractDiscreteRatesAcrossSitesTreeLikelihood::getLogLikelihoodForEachSiteForEachRateClass ( ) const [virtual, inherited]

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.

VVVdouble AbstractDiscreteRatesAcrossSitesTreeLikelihood::getLogLikelihoodForEachSiteForEachRateClassForEachState ( ) const [virtual, inherited]

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.

virtual VVdouble bpp::TreeLikelihood::getLogLikelihoodForEachSiteForEachState ( ) const [pure virtual, inherited]

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.

Implemented in bpp::AbstractTreeLikelihood.

VVdouble AbstractTreeLikelihood::getLogLikelihoodForEachSiteForEachState ( ) const [virtual, inherited]

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::AbstractTreeLikelihood::getNumberOfStates().

virtual double bpp::AbstractHomogeneousTreeLikelihood::getMaximumBranchLength ( ) const [inline, virtual, inherited]

Definition at line 244 of file AbstractHomogeneousTreeLikelihood.h.

References bpp::AbstractHomogeneousTreeLikelihood::maximumBrLen_.

virtual double bpp::AbstractHomogeneousTreeLikelihood::getMinimumBranchLength ( ) const [inline, virtual, inherited]

Definition at line 243 of file AbstractHomogeneousTreeLikelihood.h.

References bpp::AbstractHomogeneousTreeLikelihood::minimumBrLen_.

ConstBranchModelIterator* bpp::AbstractHomogeneousTreeLikelihood::getNewBranchModelIterator ( int nodeId ) const [inline, virtual, inherited]

Implements bpp::TreeLikelihood.

Definition at line 180 of file AbstractHomogeneousTreeLikelihood.h.

References bpp::AbstractHomogeneousTreeLikelihood::model_, and bpp::AbstractHomogeneousTreeLikelihood::nbDistinctSites_.

ConstSiteModelIterator* bpp::AbstractHomogeneousTreeLikelihood::getNewSiteModelIterator ( size_t siteIndex ) const [inline, virtual, inherited]

Implements bpp::TreeLikelihood.

Definition at line 185 of file AbstractHomogeneousTreeLikelihood.h.

References bpp::AbstractHomogeneousTreeLikelihood::model_, and bpp::AbstractTreeLikelihood::tree_.

ParameterList AbstractDiscreteRatesAcrossSitesTreeLikelihood::getNonDerivableParameters ( ) const [virtual, inherited]

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.

References bpp::ParameterList::addParameters().

virtual ParameterList bpp::TreeLikelihood::getNonDerivableParameters ( ) const [pure virtual, inherited]

All non derivable parameters.

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

Returns:: A ParameterList.

Implemented in bpp::RHomogeneousClockTreeLikelihood, and bpp::AbstractDiscreteRatesAcrossSitesTreeLikelihood.

size_t bpp::AbstractDiscreteRatesAcrossSitesTreeLikelihood::getNumberOfClasses ( ) const [inline, virtual, inherited]

Get the number of classes.

Returns:: The Number of classes.

Implements bpp::DiscreteRatesAcrossSitesTreeLikelihood.

Definition at line 108 of file AbstractDiscreteRatesAcrossSitesTreeLikelihood.h.

References bpp::DiscreteDistribution::getNumberOfCategories(), and bpp::AbstractDiscreteRatesAcrossSitesTreeLikelihood::rateDistribution_.

size_t bpp::AbstractTreeLikelihood::getNumberOfSites ( ) const [inline, virtual, inherited]

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_, and bpp::SiteContainer::getNumberOfSites().

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

virtual size_t bpp::TreeLikelihood::getNumberOfSites ( ) const [pure virtual, inherited]

Get the number of sites in the dataset.

Returns:: the number of sites in the dataset.

Implemented in bpp::AbstractTreeLikelihood.

size_t bpp::AbstractTreeLikelihood::getNumberOfStates ( ) const [inline, virtual, inherited]

Get the number of states in the alphabet associated to the dataset.

Returns:: the number of states in the alphabet associated to the dataset.

Implements bpp::TreeLikelihood.

Definition at line 291 of file AbstractTreeLikelihood.h.

References bpp::AbstractTreeLikelihood::data_, bpp::SiteContainer::getAlphabet(), and bpp::Alphabet::getSize().

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

virtual size_t bpp::TreeLikelihood::getNumberOfStates ( ) const [pure virtual, inherited]

Get the number of states in the alphabet associated to the dataset.

Returns:: the number of states in the alphabet associated to the dataset.

Implemented in bpp::AbstractTreeLikelihood.

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

VVdouble AbstractDiscreteRatesAcrossSitesTreeLikelihood::getPosteriorProbabilitiesOfEachRate ( ) const [virtual, inherited]

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.

Vdouble AbstractDiscreteRatesAcrossSitesTreeLikelihood::getPosteriorRateOfEachSite ( ) const [virtual, inherited]

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.

vector< size_t > AbstractDiscreteRatesAcrossSitesTreeLikelihood::getRateClassWithMaxPostProbOfEachSite ( ) const [virtual, inherited]

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.

const DiscreteDistribution* bpp::AbstractDiscreteRatesAcrossSitesTreeLikelihood::getRateDistribution ( ) const [inline, virtual, inherited]

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_.

DiscreteDistribution* bpp::AbstractDiscreteRatesAcrossSitesTreeLikelihood::getRateDistribution ( ) [inline, virtual, inherited]

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_.

ParameterList bpp::AbstractHomogeneousTreeLikelihood::getRateDistributionParameters ( ) const [inline, virtual, inherited]

Get the parameters associated to the rate distirbution.

Returns:: A ParameterList object with all rate distribution parameters.

Reimplemented from bpp::AbstractDiscreteRatesAcrossSitesTreeLikelihood.

Definition at line 171 of file AbstractHomogeneousTreeLikelihood.h.

Vdouble AbstractDiscreteRatesAcrossSitesTreeLikelihood::getRateWithMaxPostProbOfEachSite ( ) const [virtual, inherited]

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.

const std::vector<double>& bpp::AbstractHomogeneousTreeLikelihood::getRootFrequencies ( size_t siteIndex ) const [inline, virtual, inherited]

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 176 of file AbstractHomogeneousTreeLikelihood.h.

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

double RHomogeneousTreeLikelihood::getSecondOrderDerivative ( const std::string & variable ) const throw (Exception) [virtual]

Implements bpp::DerivableSecondOrder.

Reimplemented in bpp::RHomogeneousClockTreeLikelihood.

Definition at line 601 of file RHomogeneousTreeLikelihood.cpp.

double bpp::RHomogeneousTreeLikelihood::getSecondOrderDerivative	(	const std::string &	variable1,
		const std::string &	variable2
	)		const throw (Exception) `[inline, virtual]`

Implements bpp::DerivableSecondOrder.

Reimplemented in bpp::RHomogeneousClockTreeLikelihood.

Definition at line 217 of file RHomogeneousTreeLikelihood.h.

size_t bpp::RHomogeneousTreeLikelihood::getSiteIndex ( size_t site ) const throw (IndexOutOfBoundsException) [inline, virtual]

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 201 of file RHomogeneousTreeLikelihood.h.

References bpp::DRASRTreeLikelihoodData::getRootArrayPosition(), and likelihoodData_.

const SubstitutionModel* bpp::HomogeneousTreeLikelihood::getSubstitutionModel	(	int	nodeId,
		size_t	siteIndex
	)		const throw (NodeNotFoundException) `[inline, virtual, inherited]`

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 67 of file HomogeneousTreeLikelihood.h.

References bpp::HomogeneousTreeLikelihood::getSubstitutionModel().

SubstitutionModel* bpp::HomogeneousTreeLikelihood::getSubstitutionModel	(	int	nodeId,
		size_t	siteIndex
	)		throw (NodeNotFoundException) `[inline, virtual, inherited]`

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 72 of file HomogeneousTreeLikelihood.h.

References bpp::HomogeneousTreeLikelihood::getSubstitutionModel().

const SubstitutionModel* bpp::AbstractHomogeneousTreeLikelihood::getSubstitutionModel ( ) const [inline, virtual, inherited]

Returns:: The substitution model attached to this instance.

Implements bpp::HomogeneousTreeLikelihood.

Definition at line 199 of file AbstractHomogeneousTreeLikelihood.h.

References bpp::AbstractHomogeneousTreeLikelihood::model_.

SubstitutionModel* bpp::AbstractHomogeneousTreeLikelihood::getSubstitutionModel ( ) [inline, virtual, inherited]

Returns:: The substitution model attached to this instance.

Implements bpp::HomogeneousTreeLikelihood.

Definition at line 201 of file AbstractHomogeneousTreeLikelihood.h.

References bpp::AbstractHomogeneousTreeLikelihood::model_.

ParameterList AbstractHomogeneousTreeLikelihood::getSubstitutionModelParameters ( ) const [virtual, inherited]

Get the parameters associated to substitution model(s).

Returns:: A ParameterList.

Implements bpp::TreeLikelihood.

Definition at line 259 of file AbstractHomogeneousTreeLikelihood.cpp.

References bpp::ParameterList::getCommonParametersWith(), bpp::AbstractParametrizable::getParameters(), bpp::ParameterAliasable::getParameters(), bpp::AbstractTreeLikelihood::initialized_, and bpp::AbstractHomogeneousTreeLikelihood::model_.

VVdouble AbstractDiscreteRatesAcrossSitesTreeLikelihood::getTransitionProbabilities	(	int	nodeId,
		size_t	siteIndex
	)		const `[virtual, inherited]`

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.

virtual VVdouble bpp::TreeLikelihood::getTransitionProbabilities	(	int	nodeId,
		size_t	siteIndex
	)		const `[pure virtual, inherited]`

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.

Implemented in bpp::AbstractDiscreteRatesAcrossSitesTreeLikelihood.

VVVdouble bpp::AbstractHomogeneousTreeLikelihood::getTransitionProbabilitiesPerRateClass	(	int	nodeId,
		size_t	siteIndex
	)		const `[inline, virtual, inherited]`

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.

Implements bpp::DiscreteRatesAcrossSitesTreeLikelihood.

Definition at line 178 of file AbstractHomogeneousTreeLikelihood.h.

References bpp::AbstractHomogeneousTreeLikelihood::pxy_.

const Tree& bpp::AbstractTreeLikelihood::getTree ( ) const [inline, virtual, inherited]

Get the tree (topology and branch lengths).

Returns:: The tree of this TreeLikelihood object.

Implements bpp::TreeLikelihood.

Definition at line 292 of file AbstractTreeLikelihood.h.

References bpp::AbstractTreeLikelihood::tree_.

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

virtual const Tree& bpp::TreeLikelihood::getTree ( ) const [pure virtual, inherited]

Get the tree (topology and branch lengths).

Returns:: The tree of this TreeLikelihood object.

Implemented in bpp::AbstractTreeLikelihood.

Referenced by bpp::GlobalClockTreeLikelihoodFunctionWrapper::fireParameterChanged(), bpp::DRTreeLikelihoodTools::getPosteriorProbabilitiesForEachStateForEachRate(), and bpp::GlobalClockTreeLikelihoodFunctionWrapper::initParameters_().

double RHomogeneousTreeLikelihood::getValue ( ) const throw (Exception) [virtual]

Implements bpp::DerivableSecondOrder.

Definition at line 290 of file RHomogeneousTreeLikelihood.cpp.

References bpp::AbstractTreeLikelihood::isInitialized(), and minusLogLik_.

void RHomogeneousTreeLikelihood::init_ ( bool usePatterns ) throw (Exception) [private]

Method called by constructors.

Definition at line 91 of file RHomogeneousTreeLikelihood.cpp.

void AbstractHomogeneousTreeLikelihood::initBranchLengthsParameters ( ) [virtual, inherited]

Reimplemented in bpp::RHomogeneousClockTreeLikelihood.

Definition at line 307 of file AbstractHomogeneousTreeLikelihood.cpp.

References bpp::ParameterList::addParameter(), bpp::AbstractHomogeneousTreeLikelihood::brLenConstraint_, bpp::AbstractHomogeneousTreeLikelihood::brLenParameters_, bpp::ApplicationTools::displayWarning(), bpp::AbstractHomogeneousTreeLikelihood::maximumBrLen_, bpp::AbstractHomogeneousTreeLikelihood::minimumBrLen_, bpp::AbstractHomogeneousTreeLikelihood::nbNodes_, bpp::AbstractHomogeneousTreeLikelihood::nodes_, bpp::ParameterList::reset(), and bpp::TextTools::toString().

Referenced by bpp::AbstractHomogeneousTreeLikelihood::initParameters(), bpp::AbstractHomogeneousTreeLikelihood::setMaximumBranchLength(), and bpp::AbstractHomogeneousTreeLikelihood::setMinimumBranchLength().

void AbstractHomogeneousTreeLikelihood::initialize ( ) throw (Exception) [virtual, inherited]

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.

Reimplemented from bpp::AbstractTreeLikelihood.

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

Definition at line 237 of file AbstractHomogeneousTreeLikelihood.cpp.

References bpp::AbstractTreeLikelihood::data_, bpp::AbstractParametrizable::fireParameterChanged(), bpp::AbstractParametrizable::getParameters(), bpp::AbstractTreeLikelihood::initialized_, and bpp::AbstractHomogeneousTreeLikelihood::initParameters().

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

void AbstractHomogeneousTreeLikelihood::initParameters ( ) [virtual, inherited]

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

Definition at line 268 of file AbstractHomogeneousTreeLikelihood.cpp.

References bpp::AbstractParametrizable::addParameters_(), bpp::AbstractHomogeneousTreeLikelihood::brLenParameters_, bpp::DiscreteDistribution::getIndependentParameters(), bpp::ParameterAliasable::getIndependentParameters(), bpp::AbstractHomogeneousTreeLikelihood::initBranchLengthsParameters(), bpp::AbstractHomogeneousTreeLikelihood::model_, bpp::AbstractDiscreteRatesAcrossSitesTreeLikelihood::rateDistribution_, and bpp::AbstractParametrizable::resetParameters_().

Referenced by bpp::AbstractHomogeneousTreeLikelihood::initialize().

virtual bool bpp::TreeLikelihood::isInitialized ( ) const [pure virtual, inherited]

Returns:: 'true' is the likelihood function has been initialized.

Implemented in bpp::AbstractTreeLikelihood.

bool bpp::AbstractTreeLikelihood::isInitialized ( ) const [inline, virtual, inherited]

Returns:: 'true' is the likelihood function has been initialized.

Implements bpp::TreeLikelihood.

Definition at line 298 of file AbstractTreeLikelihood.h.

References bpp::AbstractTreeLikelihood::initialized_.

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

RHomogeneousTreeLikelihood & RHomogeneousTreeLikelihood::operator= ( const RHomogeneousTreeLikelihood & lik )

Definition at line 113 of file RHomogeneousTreeLikelihood.cpp.

References bpp::DRASRTreeLikelihoodData::clone(), likelihoodData_, minusLogLik_, bpp::DRASRTreeLikelihoodData::setTree(), and bpp::AbstractTreeLikelihood::tree_.

Referenced by bpp::RHomogeneousMixedTreeLikelihood::operator=().

void AbstractDiscreteRatesAcrossSitesTreeLikelihood::resetLikelihoodArray ( VVVdouble & likelihoodArray ) [static, inherited]

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().

void RHomogeneousTreeLikelihood::setData ( const SiteContainer & sites ) throw (Exception) [virtual]

Set the dataset for which the likelihood must be evaluated.

Parameters:

sites The data set to use.

Implements bpp::TreeLikelihood.

Reimplemented in bpp::RHomogeneousMixedTreeLikelihood.

Definition at line 133 of file RHomogeneousTreeLikelihood.cpp.

References bpp::ApplicationTools::displayResult(), bpp::ApplicationTools::displayTask(), bpp::ApplicationTools::displayTaskDone(), bpp::PatternTools::getSequenceSubset(), and bpp::TextTools::toString().

Referenced by bpp::RHomogeneousMixedTreeLikelihood::setData().

virtual void bpp::AbstractHomogeneousTreeLikelihood::setMaximumBranchLength ( double maximum ) throw (Exception) [inline, virtual, inherited]

Reimplemented in bpp::RHomogeneousMixedTreeLikelihood.

Definition at line 233 of file AbstractHomogeneousTreeLikelihood.h.

References bpp::AbstractHomogeneousTreeLikelihood::brLenConstraint_, bpp::AbstractHomogeneousTreeLikelihood::initBranchLengthsParameters(), bpp::AbstractHomogeneousTreeLikelihood::maximumBrLen_, bpp::AbstractHomogeneousTreeLikelihood::minimumBrLen_, and bpp::TextTools::toString().

virtual void bpp::AbstractHomogeneousTreeLikelihood::setMinimumBranchLength ( double minimum ) throw (Exception) [inline, virtual, inherited]

Reimplemented in bpp::RHomogeneousMixedTreeLikelihood.

Definition at line 223 of file AbstractHomogeneousTreeLikelihood.h.

References bpp::AbstractHomogeneousTreeLikelihood::brLenConstraint_, bpp::AbstractHomogeneousTreeLikelihood::initBranchLengthsParameters(), bpp::AbstractHomogeneousTreeLikelihood::maximumBrLen_, bpp::AbstractHomogeneousTreeLikelihood::minimumBrLen_, and bpp::TextTools::toString().

void RHomogeneousTreeLikelihood::setParameters ( const ParameterList & parameters ) throw (ParameterNotFoundException, ConstraintException) [virtual]

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.

Implements bpp::DerivableSecondOrder.

Definition at line 250 of file RHomogeneousTreeLikelihood.cpp.

void AbstractHomogeneousTreeLikelihood::setSubstitutionModel ( SubstitutionModel * model ) throw (Exception) [virtual, inherited]

Returns:: Set the substitution model for this instance.

Exceptions:

Exception If the model could not be set (for instance, because of a wrong alphabet type).

Implements bpp::HomogeneousTreeLikelihood.

Definition at line 172 of file AbstractHomogeneousTreeLikelihood.cpp.

References bpp::Node::getId().

Friends And Related Function Documentation

friend class RHomogeneousMixedTreeLikelihood [friend]

Definition at line 269 of file RHomogeneousTreeLikelihood.h.

Member Data Documentation

std::auto_ptr<Constraint> bpp::AbstractHomogeneousTreeLikelihood::brLenConstraint_ [protected, inherited]

Definition at line 118 of file AbstractHomogeneousTreeLikelihood.h.

Referenced by bpp::AbstractHomogeneousTreeLikelihood::initBranchLengthsParameters(), bpp::AbstractHomogeneousTreeLikelihood::operator=(), bpp::AbstractHomogeneousTreeLikelihood::setMaximumBranchLength(), and bpp::AbstractHomogeneousTreeLikelihood::setMinimumBranchLength().

ParameterList bpp::AbstractHomogeneousTreeLikelihood::brLenParameters_ [protected, inherited]

Definition at line 89 of file AbstractHomogeneousTreeLikelihood.h.

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

bool bpp::AbstractTreeLikelihood::computeFirstOrderDerivatives_ [protected, inherited]

Definition at line 227 of file AbstractTreeLikelihood.h.

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

bool bpp::AbstractTreeLikelihood::computeSecondOrderDerivatives_ [protected, inherited]

Definition at line 228 of file AbstractTreeLikelihood.h.

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

std::map<int, VVVdouble> bpp::AbstractHomogeneousTreeLikelihood::d2pxy_ [mutable, protected, inherited]

Definition at line 95 of file AbstractHomogeneousTreeLikelihood.h.

Referenced by bpp::AbstractHomogeneousTreeLikelihood::computeTransitionProbabilitiesForNode(), computeTreeD2Likelihood(), bpp::DRHomogeneousTreeLikelihood::computeTreeD2LikelihoodAtNode(), and bpp::AbstractHomogeneousTreeLikelihood::operator=().

const SiteContainer* bpp::AbstractTreeLikelihood::data_ [protected, inherited]

Definition at line 225 of file AbstractTreeLikelihood.h.

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

std::map<int, VVVdouble> bpp::AbstractHomogeneousTreeLikelihood::dpxy_ [mutable, protected, inherited]

Definition at line 93 of file AbstractHomogeneousTreeLikelihood.h.

Referenced by bpp::AbstractHomogeneousTreeLikelihood::computeTransitionProbabilitiesForNode(), computeTreeDLikelihood(), bpp::DRHomogeneousTreeLikelihood::computeTreeDLikelihoodAtNode(), and bpp::AbstractHomogeneousTreeLikelihood::operator=().

bool bpp::AbstractTreeLikelihood::initialized_ [protected, inherited]

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=().

double bpp::AbstractHomogeneousTreeLikelihood::maximumBrLen_ [protected, inherited]

Definition at line 117 of file AbstractHomogeneousTreeLikelihood.h.

Referenced by bpp::AbstractHomogeneousTreeLikelihood::getMaximumBranchLength(), bpp::AbstractHomogeneousTreeLikelihood::initBranchLengthsParameters(), bpp::AbstractHomogeneousTreeLikelihood::operator=(), bpp::AbstractHomogeneousTreeLikelihood::setMaximumBranchLength(), and bpp::AbstractHomogeneousTreeLikelihood::setMinimumBranchLength().

double bpp::AbstractHomogeneousTreeLikelihood::minimumBrLen_ [protected, inherited]

Definition at line 116 of file AbstractHomogeneousTreeLikelihood.h.

Referenced by bpp::AbstractHomogeneousTreeLikelihood::getMinimumBranchLength(), bpp::AbstractHomogeneousTreeLikelihood::initBranchLengthsParameters(), bpp::AbstractHomogeneousTreeLikelihood::operator=(), bpp::AbstractHomogeneousTreeLikelihood::setMaximumBranchLength(), and bpp::AbstractHomogeneousTreeLikelihood::setMinimumBranchLength().

double bpp::RHomogeneousTreeLikelihood::minusLogLik_ [protected]

Definition at line 90 of file RHomogeneousTreeLikelihood.h.

Referenced by bpp::RHomogeneousMixedTreeLikelihood::fireParameterChanged(), fireParameterChanged(), getValue(), and operator=().

SubstitutionModel* bpp::AbstractHomogeneousTreeLikelihood::model_ [protected, inherited]

Definition at line 88 of file AbstractHomogeneousTreeLikelihood.h.

size_t bpp::AbstractHomogeneousTreeLikelihood::nbClasses_ [protected, inherited]

Definition at line 108 of file AbstractHomogeneousTreeLikelihood.h.

size_t bpp::AbstractHomogeneousTreeLikelihood::nbDistinctSites_ [protected, inherited]

Definition at line 108 of file AbstractHomogeneousTreeLikelihood.h.

size_t bpp::AbstractHomogeneousTreeLikelihood::nbNodes_ [protected, inherited]

Definition at line 108 of file AbstractHomogeneousTreeLikelihood.h.

Referenced by bpp::AbstractHomogeneousTreeLikelihood::applyParameters(), bpp::AbstractHomogeneousTreeLikelihood::computeAllTransitionProbabilities(), bpp::DRHomogeneousTreeLikelihood::computeTreeD2Likelihoods(), bpp::DRHomogeneousTreeLikelihood::computeTreeDLikelihoods(), bpp::AbstractHomogeneousTreeLikelihood::initBranchLengthsParameters(), and bpp::AbstractHomogeneousTreeLikelihood::operator=().

size_t bpp::AbstractHomogeneousTreeLikelihood::nbSites_ [protected, inherited]

Definition at line 108 of file AbstractHomogeneousTreeLikelihood.h.

Referenced by getD2LogLikelihood(), getDLogLikelihood(), getLikelihood(), getLogLikelihood(), and bpp::AbstractHomogeneousTreeLikelihood::operator=().

size_t bpp::AbstractHomogeneousTreeLikelihood::nbStates_ [protected, inherited]

Definition at line 108 of file AbstractHomogeneousTreeLikelihood.h.

std::vector<Node*> bpp::AbstractHomogeneousTreeLikelihood::nodes_ [protected, inherited]

Pointer toward all nodes in the tree.

The position in the array is the number used in the parameter name. This may be different from the node id, unless you used the resetNodeId method on the input tree.

Definition at line 105 of file AbstractHomogeneousTreeLikelihood.h.

Referenced by bpp::AbstractHomogeneousTreeLikelihood::AbstractHomogeneousTreeLikelihood(), bpp::AbstractHomogeneousTreeLikelihood::applyParameters(), bpp::AbstractHomogeneousTreeLikelihood::computeAllTransitionProbabilities(), computeTreeD2Likelihood(), bpp::DRHomogeneousTreeLikelihood::computeTreeD2Likelihoods(), computeTreeDLikelihood(), bpp::DRHomogeneousTreeLikelihood::computeTreeDLikelihoods(), bpp::DRHomogeneousTreeLikelihood::fireParameterChanged(), fireParameterChanged(), bpp::AbstractHomogeneousTreeLikelihood::initBranchLengthsParameters(), and bpp::AbstractHomogeneousTreeLikelihood::operator=().