A class to compute the average of several DRHomogeneousTreeLikelihood defined from a Mixed Substitution Model. More...

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

Inheritance diagram for bpp::DRHomogeneousMixedTreeLikelihood:

Collaboration diagram for bpp::DRHomogeneousMixedTreeLikelihood:

Public Member Functions
	DRHomogeneousMixedTreeLikelihood (const Tree &tree, SubstitutionModel model, DiscreteDistribution rDist, bool checkRooted=true, bool verbose=true, bool rootArray=false) throw (Exception)
	Build a new DRHomogeneousMixedTreeLikelihood object without data.
	DRHomogeneousMixedTreeLikelihood (const Tree &tree, const SiteContainer &data, SubstitutionModel model, DiscreteDistribution rDist, bool checkRooted=true, bool verbose=true, bool rootArray=false) throw (Exception)
	Build a new DRHomogeneousMixedTreeLikelihood object with data.
	DRHomogeneousMixedTreeLikelihood (const DRHomogeneousMixedTreeLikelihood &lik)
DRHomogeneousMixedTreeLikelihood &	operator= (const DRHomogeneousMixedTreeLikelihood &lik)
virtual	~DRHomogeneousMixedTreeLikelihood ()
DRHomogeneousMixedTreeLikelihood *	clone () const
void	initialize () throw (Exception)
	Init the likelihood object.
void	fireParameterChanged (const ParameterList &params)
void	computeTreeLikelihood ()
virtual void	computeTreeDLikelihoods ()
void	setParameters (const ParameterList &parameters) throw (ParameterNotFoundException, ConstraintException)
	Implements the Function interface.
double	getValue () const throw (Exception)
	Function and NNISearchable interface.
DRASDRTreeLikelihoodData *	getLikelihoodData ()
const DRASDRTreeLikelihoodData *	getLikelihoodData () const
virtual void	computeLikelihoodAtNode (int nodeId, VVVdouble &likelihoodArray) const
	Compute the likelihood array at a given node.
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 DRHomogeneousTreeLikelihood class.
double	getLikelihood () const
	Get the likelihood for the whole dataset.
double	getLogLikelihood () const
	Get the logarithm of the likelihood for the whole dataset.
void	setData (const SiteContainer &sites) throw (Exception)
	Set the dataset for which the likelihood must be evaluated.
double	getLikelihoodForASite (unsigned int site) const
double	getLogLikelihoodForASite (unsigned int site) const
The DiscreteRatesAcrossSites interface implementation:
double	getLikelihoodForASiteForARateClass (unsigned int site, unsigned int rateClass) const
double	getLogLikelihoodForASiteForARateClass (unsigned int site, unsigned int rateClass) const
double	getLikelihoodForASiteForARateClassForAState (unsigned int site, unsigned int rateClass, int state) const
double	getLogLikelihoodForASiteForARateClassForAState (unsigned int site, unsigned int rateClass, int state) const
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	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.
size_t	getSiteIndex (size_t site) const throw (IndexOutOfBoundsException)
	Get the index (used for inner computations) of a given site (original alignment column).
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.
The TreeLikelihood interface.
Other methods are implemented in the AbstractTreeLikelihood class.
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	computeLikelihoodAtNode_ (const Node *node, VVVdouble &likelihoodArray) const
virtual void	computeSubtreeLikelihoodPostfix (const Node *node)
	Compute the likelihood for a subtree defined by the Tree::Node node.
virtual void	computeSubtreeLikelihoodPrefix (const Node *node)
virtual void	computeRootLikelihood ()
virtual void	computeTreeD2LikelihoodAtNode (const Node *)
virtual void	computeTreeD2Likelihoods ()
void	resetLikelihoodArrays (const Node *node)
virtual void	displayLikelihood (const Node *node)
	This method is mainly for debugging purpose.
virtual void	computeTreeDLikelihoodAtNode (const Node *node)
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_ ()
Static Protected Member Functions
static void	computeLikelihoodFromArrays (const std::vector< const VVVdouble * > &iLik, const std::vector< const VVVdouble * > &tProb, VVVdouble &oLik, size_t nbNodes, size_t nbDistinctSites, size_t nbClasses, size_t nbStates, bool reset=true)
	Compute conditional likelihoods.
static void	computeLikelihoodFromArrays (const std::vector< const VVVdouble * > &iLik, const std::vector< const VVVdouble * > &tProb, const VVVdouble iLikR, const VVVdouble tProbR, VVVdouble &oLik, size_t nbNodes, size_t nbDistinctSites, size_t nbClasses, size_t nbStates, bool reset=true)
	Compute conditional likelihoods.
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 Attributes
std::vector < DRHomogeneousTreeLikelihood * >	treeLikelihoodsContainer_
std::vector< double >	probas_
bool	rootArray_
Friends
class	DRHomogeneousMixedTreeLikelihood

Detailed Description

A class to compute the average of several DRHomogeneousTreeLikelihood defined from a Mixed Substitution Model.

In all computations, the average of the likelihoods, probabilities are computed.

Definition at line 60 of file DRHomogeneousMixedTreeLikelihood.h.

Constructor & Destructor Documentation

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

Build a new DRHomogeneousMixedTreeLikelihood 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 mixed 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?
rootArray	is true if the array of the likelihoods at the root should be computed (useful for ancestral reconstruction).

Exceptions:

Exception in an error occured.

Definition at line 54 of file DRHomogeneousMixedTreeLikelihood.cpp.

References bpp::MixedSubstitutionModel::getNModel(), bpp::MixedSubstitutionModel::getNProbability(), and bpp::MixedSubstitutionModel::getNumberOfModels().

Referenced by clone().

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

Build a new DRHomogeneousMixedTreeLikelihood object with data.

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

Parameters:

tree	The tree to use.
data	Sequences to use.
model	The mixed 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?
rootArray	is true if the array of the likelihoods at the root should be computed (useful for ancestral reconstruction).

Exceptions:

Exception in an error occured.

Definition at line 80 of file DRHomogeneousMixedTreeLikelihood.cpp.

References bpp::MixedSubstitutionModel::getNModel(), bpp::MixedSubstitutionModel::getNProbability(), and bpp::MixedSubstitutionModel::getNumberOfModels().

DRHomogeneousMixedTreeLikelihood::DRHomogeneousMixedTreeLikelihood ( const DRHomogeneousMixedTreeLikelihood & lik )

Definition at line 129 of file DRHomogeneousMixedTreeLikelihood.cpp.

References probas_, and treeLikelihoodsContainer_.

DRHomogeneousMixedTreeLikelihood::~DRHomogeneousMixedTreeLikelihood ( ) [virtual]

Definition at line 142 of file DRHomogeneousMixedTreeLikelihood.cpp.

References treeLikelihoodsContainer_.

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(), fireParameterChanged(), bpp::DRHomogeneousTreeLikelihood::fireParameterChanged(), and bpp::RHomogeneousTreeLikelihood::fireParameterChanged().

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

Reimplemented from bpp::DRHomogeneousTreeLikelihood.

Definition at line 132 of file DRHomogeneousMixedTreeLikelihood.h.

References DRHomogeneousMixedTreeLikelihood().

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 bpp::RHomogeneousTreeLikelihood::fireParameterChanged().

virtual void bpp::DRHomogeneousTreeLikelihood::computeLikelihoodAtNode	(	int	nodeId,
		VVVdouble &	likelihoodArray
	)		const `[inline, virtual, inherited]`

Compute the likelihood array at a given node.

Parameters:

nodeId	The id of the node to consider.
likelihoodArray	The array where to store the results.

Implements bpp::DRTreeLikelihood.

Definition at line 209 of file DRHomogeneousTreeLikelihood.h.

References bpp::DRHomogeneousTreeLikelihood::computeLikelihoodAtNode_(), bpp::TreeTemplate< N >::getNode(), and bpp::AbstractTreeLikelihood::tree_.

void DRHomogeneousMixedTreeLikelihood::computeLikelihoodAtNode_	(	const Node *	node,
		VVVdouble &	likelihoodArray
	)		const `[protected, virtual]`

Reimplemented from bpp::DRHomogeneousTreeLikelihood.

Definition at line 352 of file DRHomogeneousMixedTreeLikelihood.cpp.

References bpp::AbstractHomogeneousTreeLikelihood::nbClasses_, bpp::AbstractHomogeneousTreeLikelihood::nbDistinctSites_, bpp::AbstractHomogeneousTreeLikelihood::nbStates_, probas_, and treeLikelihoodsContainer_.

void DRHomogeneousTreeLikelihood::computeLikelihoodFromArrays	(	const std::vector< const VVVdouble * > &	iLik,
		const std::vector< const VVVdouble * > &	tProb,
		VVVdouble &	oLik,
		size_t	nbNodes,
		size_t	nbDistinctSites,
		size_t	nbClasses,
		size_t	nbStates,
		bool	reset = `true`
	)		`[static, protected, inherited]`

Compute conditional likelihoods.

This method is the "core" likelihood computation function, performing all the product uppon all nodes, the summation for each ancestral state and each rate class. It is designed for inner usage, and a maximum efficiency, so no checking is performed on the input parameters. Use with care!

Parameters:

iLik	A vector of likelihood arrays, one for each conditional node.
tProb	A vector of transition probabilities, one for each node.
oLik	The likelihood array to store the computed likelihoods.
nbNodes	The number of nodes = the size of the input vectors.
nbDistinctSites	The number of distinct sites (the first dimension of the likelihood array).
nbClasses	The number of rate classes (the second dimension of the likelihood array).
nbStates	The number of states (the third dimension of the likelihood array).
reset	Tell if the output likelihood array must be initalized prior to computation. If true, the resetLikelihoodArray method will be called.

Definition at line 827 of file DRHomogeneousTreeLikelihood.cpp.

References bpp::AbstractDiscreteRatesAcrossSitesTreeLikelihood::resetLikelihoodArray().

Referenced by bpp::DRHomogeneousTreeLikelihood::computeLikelihoodAtNode_(), bpp::DRHomogeneousTreeLikelihood::computeRootLikelihood(), bpp::DRHomogeneousTreeLikelihood::computeSubtreeLikelihoodPostfix(), and bpp::DRHomogeneousTreeLikelihood::computeSubtreeLikelihoodPrefix().

void DRHomogeneousTreeLikelihood::computeLikelihoodFromArrays	(	const std::vector< const VVVdouble * > &	iLik,
		const std::vector< const VVVdouble * > &	tProb,
		const VVVdouble *	iLikR,
		const VVVdouble *	tProbR,
		VVVdouble &	oLik,
		size_t	nbNodes,
		size_t	nbDistinctSites,
		size_t	nbClasses,
		size_t	nbStates,
		bool	reset = `true`
	)		`[static, protected, inherited]`

Compute conditional likelihoods.

This method is the "core" likelihood computation function, performing all the product uppon all nodes, the summation for each ancestral state and each rate class. This function is specific to non-reversible models: the subtree containing the root is specified separately. It is designed for inner usage, and a maximum efficiency, so no checking is performed on the input parameters. Use with care!

Parameters:

iLik	A vector of likelihood arrays, one for each conditional node.
tProb	A vector of transition probabilities, one for each node.
iLikR	The likelihood array for the subtree containing the root of the tree.
tProbR	The transition probabilities for thr subtree containing the root of the tree.
oLik	The likelihood array to store the computed likelihoods.
nbNodes	The number of nodes = the size of the input vectors.
nbDistinctSites	The number of distinct sites (the first dimension of the likelihood array).
nbClasses	The number of rate classes (the second dimension of the likelihood array).
nbStates	The number of states (the third dimension of the likelihood array).
reset	Tell if the output likelihood array must be initalized prior to computation. If true, the resetLikelihoodArray method will be called.

Definition at line 876 of file DRHomogeneousTreeLikelihood.cpp.

References bpp::AbstractDiscreteRatesAcrossSitesTreeLikelihood::resetLikelihoodArray().

void DRHomogeneousMixedTreeLikelihood::computeRootLikelihood ( ) [protected, virtual]

Reimplemented from bpp::DRHomogeneousTreeLikelihood.

Definition at line 344 of file DRHomogeneousMixedTreeLikelihood.cpp.

References treeLikelihoodsContainer_.

Referenced by computeTreeLikelihood(), and initialize().

void DRHomogeneousMixedTreeLikelihood::computeSubtreeLikelihoodPostfix ( 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 from bpp::DRHomogeneousTreeLikelihood.

Definition at line 328 of file DRHomogeneousMixedTreeLikelihood.cpp.

References treeLikelihoodsContainer_.

void DRHomogeneousMixedTreeLikelihood::computeSubtreeLikelihoodPrefix ( const Node * node ) [protected, virtual]

This method initilize the remaining likelihood arrays, corresponding to father nodes. It must be called after the postfix method because it requires that the arrays for son nodes to be be computed.

Reimplemented from bpp::DRHomogeneousTreeLikelihood.

Definition at line 336 of file DRHomogeneousMixedTreeLikelihood.cpp.

References treeLikelihoodsContainer_.

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 bpp::RHomogeneousTreeLikelihood::fireParameterChanged().

void DRHomogeneousMixedTreeLikelihood::computeTreeD2LikelihoodAtNode ( const Node * node ) [protected, virtual]

Reimplemented from bpp::DRHomogeneousTreeLikelihood.

Definition at line 448 of file DRHomogeneousMixedTreeLikelihood.cpp.

References treeLikelihoodsContainer_.

void DRHomogeneousMixedTreeLikelihood::computeTreeD2Likelihoods ( ) [protected, virtual]

Reimplemented from bpp::DRHomogeneousTreeLikelihood.

Definition at line 456 of file DRHomogeneousMixedTreeLikelihood.cpp.

References treeLikelihoodsContainer_.

void DRHomogeneousTreeLikelihood::computeTreeDLikelihoodAtNode ( const Node * node ) [protected, virtual, inherited]

Definition at line 291 of file DRHomogeneousTreeLikelihood.cpp.

References bpp::DRHomogeneousTreeLikelihood::computeLikelihoodAtNode_(), bpp::AbstractHomogeneousTreeLikelihood::dpxy_, bpp::DRASDRTreeLikelihoodData::getDLikelihoodArray(), bpp::Node::getFather(), bpp::Node::getId(), bpp::DRASDRTreeLikelihoodData::getLikelihoodArray(), bpp::DiscreteDistribution::getProbability(), bpp::DRASDRTreeLikelihoodData::getRootRateSiteLikelihoodArray(), bpp::DRHomogeneousTreeLikelihood::likelihoodData_, bpp::AbstractHomogeneousTreeLikelihood::nbClasses_, bpp::AbstractHomogeneousTreeLikelihood::nbDistinctSites_, bpp::AbstractHomogeneousTreeLikelihood::nbStates_, bpp::AbstractHomogeneousTreeLikelihood::pxy_, and bpp::AbstractDiscreteRatesAcrossSitesTreeLikelihood::rateDistribution_.

Referenced by bpp::DRHomogeneousTreeLikelihood::computeTreeDLikelihoods().

void DRHomogeneousMixedTreeLikelihood::computeTreeDLikelihoods ( ) [virtual]

Reimplemented from bpp::DRHomogeneousTreeLikelihood.

Definition at line 392 of file DRHomogeneousMixedTreeLikelihood.cpp.

References treeLikelihoodsContainer_.

void DRHomogeneousMixedTreeLikelihood::computeTreeLikelihood ( )

Reimplemented from bpp::DRHomogeneousTreeLikelihood.

Definition at line 203 of file DRHomogeneousMixedTreeLikelihood.cpp.

References computeRootLikelihood(), rootArray_, and treeLikelihoodsContainer_.

void DRHomogeneousMixedTreeLikelihood::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 from bpp::DRHomogeneousTreeLikelihood.

Definition at line 515 of file DRHomogeneousMixedTreeLikelihood.cpp.

References treeLikelihoodsContainer_.

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(), bpp::RHomogeneousTreeLikelihood::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 DRHomogeneousMixedTreeLikelihood::fireParameterChanged ( const ParameterList & params ) [virtual]

Reimplemented from bpp::DRHomogeneousTreeLikelihood.

Definition at line 173 of file DRHomogeneousMixedTreeLikelihood.cpp.

References bpp::ParameterList::addParameters(), bpp::AbstractHomogeneousTreeLikelihood::applyParameters(), getLogLikelihood(), bpp::MixedSubstitutionModel::getNModel(), bpp::MixedSubstitutionModel::getNumberOfModels(), bpp::AbstractParametrizable::getParameters(), bpp::ParameterAliasable::getParameters(), bpp::MixedSubstitutionModel::getProbabilities(), bpp::ParameterList::includeParameters(), bpp::DRHomogeneousTreeLikelihood::minusLogLik_, bpp::AbstractHomogeneousTreeLikelihood::model_, probas_, and treeLikelihoodsContainer_.

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_.

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

Reimplemented from bpp::DRHomogeneousTreeLikelihood.

Definition at line 400 of file DRHomogeneousMixedTreeLikelihood.cpp.

double DRHomogeneousMixedTreeLikelihood::getLikelihood ( ) const [virtual]

Get the likelihood for the whole dataset.

Returns:: The likelihood of the dataset.

Reimplemented from bpp::DRHomogeneousTreeLikelihood.

Definition at line 217 of file DRHomogeneousMixedTreeLikelihood.cpp.

References bpp::DRASDRTreeLikelihoodData::getRootRateSiteLikelihoodArray(), bpp::AbstractTreeLikelihoodData::getWeights(), bpp::DRHomogeneousTreeLikelihood::likelihoodData_, bpp::AbstractHomogeneousTreeLikelihood::nbDistinctSites_, probas_, and treeLikelihoodsContainer_.

DRASDRTreeLikelihoodData* bpp::DRHomogeneousTreeLikelihood::getLikelihoodData ( ) [inline, virtual, inherited]

Returns:: The underlying likelihood data structure.

Implements bpp::DRTreeLikelihood.

Definition at line 206 of file DRHomogeneousTreeLikelihood.h.

References bpp::DRHomogeneousTreeLikelihood::likelihoodData_.

Referenced by bpp::NNIHomogeneousTreeLikelihood::setData(), and bpp::NNIHomogeneousTreeLikelihood::topologyChangeTested().

const DRASDRTreeLikelihoodData* bpp::DRHomogeneousTreeLikelihood::getLikelihoodData ( ) const [inline, virtual, inherited]

Returns:: The underlying likelihood data structure.

Implements bpp::DRTreeLikelihood.

Definition at line 207 of file DRHomogeneousTreeLikelihood.h.

References bpp::DRHomogeneousTreeLikelihood::likelihoodData_.

double DRHomogeneousMixedTreeLikelihood::getLikelihoodForASite ( unsigned int site ) const

Definition at line 272 of file DRHomogeneousMixedTreeLikelihood.cpp.

References probas_, and treeLikelihoodsContainer_.

Referenced by getLogLikelihoodForASite().

double DRHomogeneousTreeLikelihood::getLikelihoodForASite ( size_t site ) const [virtual, inherited]

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 192 of file DRHomogeneousTreeLikelihood.cpp.

References bpp::AbstractTreeLikelihoodData::getRootArrayPosition(), bpp::DRASDRTreeLikelihoodData::getRootRateSiteLikelihoodArray(), and bpp::DRHomogeneousTreeLikelihood::likelihoodData_.

double DRHomogeneousMixedTreeLikelihood::getLikelihoodForASiteForARateClass	(	unsigned int	site,
		unsigned int	rateClass
	)		const

Definition at line 290 of file DRHomogeneousMixedTreeLikelihood.cpp.

References probas_, and treeLikelihoodsContainer_.

Referenced by getLogLikelihoodForASiteForARateClass().

double DRHomogeneousTreeLikelihood::getLikelihoodForASiteForARateClass	(	size_t	site,
		size_t	rateClass
	)		const `[virtual, inherited]`

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 205 of file DRHomogeneousTreeLikelihood.cpp.

References bpp::AbstractTreeLikelihoodData::getRootArrayPosition(), bpp::DRASDRTreeLikelihoodData::getRootSiteLikelihoodArray(), and bpp::DRHomogeneousTreeLikelihood::likelihoodData_.

double DRHomogeneousMixedTreeLikelihood::getLikelihoodForASiteForARateClassForAState	(	unsigned int	site,
		unsigned int	rateClass,
		int	state
	)		const

Definition at line 308 of file DRHomogeneousMixedTreeLikelihood.cpp.

References probas_, and treeLikelihoodsContainer_.

Referenced by getLogLikelihoodForASiteForARateClassForAState().

double DRHomogeneousTreeLikelihood::getLikelihoodForASiteForARateClassForAState	(	size_t	site,
		size_t	rateClass,
		int	state
	)		const `[virtual, inherited]`

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 219 of file DRHomogeneousTreeLikelihood.cpp.

References bpp::AbstractTreeLikelihoodData::getRootArrayPosition(), bpp::DRASDRTreeLikelihoodData::getRootLikelihoodArray(), and bpp::DRHomogeneousTreeLikelihood::likelihoodData_.

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 DRHomogeneousMixedTreeLikelihood::getLogLikelihood ( ) const [virtual]

Get the logarithm of the likelihood for the whole dataset.

Returns:: The logarithm of the likelihood of the dataset.

Reimplemented from bpp::DRHomogeneousTreeLikelihood.

Definition at line 240 of file DRHomogeneousMixedTreeLikelihood.cpp.

References bpp::DRASDRTreeLikelihoodData::getRootRateSiteLikelihoodArray(), bpp::AbstractTreeLikelihoodData::getWeights(), bpp::DRHomogeneousTreeLikelihood::likelihoodData_, bpp::AbstractHomogeneousTreeLikelihood::nbDistinctSites_, probas_, and treeLikelihoodsContainer_.

Referenced by fireParameterChanged().

double DRHomogeneousMixedTreeLikelihood::getLogLikelihoodForASite ( unsigned int site ) const

Definition at line 283 of file DRHomogeneousMixedTreeLikelihood.cpp.

References getLikelihoodForASite().

double DRHomogeneousTreeLikelihood::getLogLikelihoodForASite ( size_t site ) const [virtual, inherited]

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 199 of file DRHomogeneousTreeLikelihood.cpp.

References bpp::AbstractTreeLikelihoodData::getRootArrayPosition(), bpp::DRASDRTreeLikelihoodData::getRootRateSiteLikelihoodArray(), and bpp::DRHomogeneousTreeLikelihood::likelihoodData_.

double DRHomogeneousMixedTreeLikelihood::getLogLikelihoodForASiteForARateClass	(	unsigned int	site,
		unsigned int	rateClass
	)		const

Definition at line 301 of file DRHomogeneousMixedTreeLikelihood.cpp.

References getLikelihoodForASiteForARateClass().

double DRHomogeneousTreeLikelihood::getLogLikelihoodForASiteForARateClass	(	size_t	site,
		size_t	rateClass
	)		const `[virtual, inherited]`

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 212 of file DRHomogeneousTreeLikelihood.cpp.

References bpp::AbstractTreeLikelihoodData::getRootArrayPosition(), bpp::DRASDRTreeLikelihoodData::getRootSiteLikelihoodArray(), and bpp::DRHomogeneousTreeLikelihood::likelihoodData_.

double DRHomogeneousMixedTreeLikelihood::getLogLikelihoodForASiteForARateClassForAState	(	unsigned int	site,
		unsigned int	rateClass,
		int	state
	)		const

Definition at line 320 of file DRHomogeneousMixedTreeLikelihood.cpp.

References getLikelihoodForASiteForARateClassForAState().

double DRHomogeneousTreeLikelihood::getLogLikelihoodForASiteForARateClassForAState	(	size_t	site,
		size_t	rateClass,
		int	state
	)		const `[virtual, inherited]`

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 226 of file DRHomogeneousTreeLikelihood.cpp.

References bpp::AbstractTreeLikelihoodData::getRootArrayPosition(), bpp::DRASDRTreeLikelihoodData::getRootLikelihoodArray(), and bpp::DRHomogeneousTreeLikelihood::likelihoodData_.

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

Reimplemented from bpp::DRHomogeneousTreeLikelihood.

Definition at line 464 of file DRHomogeneousMixedTreeLikelihood.cpp.

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

Reimplemented from bpp::DRHomogeneousTreeLikelihood.

Definition at line 176 of file DRHomogeneousMixedTreeLikelihood.h.

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

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 152 of file DRHomogeneousTreeLikelihood.h.

References bpp::AbstractTreeLikelihoodData::getRootArrayPosition(), and bpp::DRHomogeneousTreeLikelihood::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_.

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_().

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().

double DRHomogeneousTreeLikelihood::getValue ( ) const throw (Exception) [virtual, inherited]

Function and NNISearchable interface.

Implements bpp::DerivableSecondOrder.

Definition at line 280 of file DRHomogeneousTreeLikelihood.cpp.

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

Referenced by bpp::NNIHomogeneousTreeLikelihood::getTopologyValue().

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 DRHomogeneousMixedTreeLikelihood::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.

Reimplemented from bpp::AbstractHomogeneousTreeLikelihood.

Definition at line 151 of file DRHomogeneousMixedTreeLikelihood.cpp.

References computeRootLikelihood(), rootArray_, and treeLikelihoodsContainer_.

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::ParameterAliasable::getIndependentParameters(), bpp::DiscreteDistribution::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(), bpp::RHomogeneousTreeLikelihood::getValue(), and bpp::RNonHomogeneousTreeLikelihood::getValue().

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

Definition at line 111 of file DRHomogeneousMixedTreeLikelihood.cpp.

References bpp::DRHomogeneousTreeLikelihood::operator=(), probas_, rootArray_, and treeLikelihoodsContainer_.

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 DRHomogeneousMixedTreeLikelihood::resetLikelihoodArrays ( const Node * node ) [protected, virtual]

Reimplemented from bpp::DRHomogeneousTreeLikelihood.

Definition at line 195 of file DRHomogeneousMixedTreeLikelihood.cpp.

References treeLikelihoodsContainer_.

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

Set the dataset for which the likelihood must be evaluated.

Parameters:

sites The data set to use.

Reimplemented from bpp::DRHomogeneousTreeLikelihood.

Definition at line 162 of file DRHomogeneousMixedTreeLikelihood.cpp.

References bpp::DRHomogeneousTreeLikelihood::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 DRHomogeneousTreeLikelihood::setParameters ( const ParameterList & parameters ) throw (ParameterNotFoundException, ConstraintException) [virtual, inherited]

Implements the Function interface.

Update the parameter list and call the fireParameterChanged() 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 233 of file DRHomogeneousTreeLikelihood.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 DRHomogeneousMixedTreeLikelihood [friend, inherited]

Definition at line 306 of file DRHomogeneousTreeLikelihood.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(), bpp::RHomogeneousTreeLikelihood::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(), bpp::RHomogeneousTreeLikelihood::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::DRHomogeneousTreeLikelihood::minusLogLik_ [protected, inherited]

Definition at line 72 of file DRHomogeneousTreeLikelihood.h.

Referenced by bpp::DRHomogeneousTreeLikelihood::DRHomogeneousTreeLikelihood(), fireParameterChanged(), bpp::DRHomogeneousTreeLikelihood::fireParameterChanged(), bpp::DRHomogeneousTreeLikelihood::getValue(), and bpp::DRHomogeneousTreeLikelihood::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 bpp::RHomogeneousTreeLikelihood::getD2LogLikelihood(), bpp::RHomogeneousTreeLikelihood::getDLogLikelihood(), bpp::RHomogeneousTreeLikelihood::getLikelihood(), bpp::RHomogeneousTreeLikelihood::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(), bpp::RHomogeneousTreeLikelihood::computeTreeD2Likelihood(), bpp::DRHomogeneousTreeLikelihood::computeTreeD2Likelihoods(), bpp::RHomogeneousTreeLikelihood::computeTreeDLikelihood(), bpp::DRHomogeneousTreeLikelihood::computeTreeDLikelihoods(), bpp::DRHomogeneousTreeLikelihood::fireParameterChanged(), bpp::RHomogeneousTreeLikelihood::fireParameterChanged(), bpp::AbstractHomogeneousTreeLikelihood::initBranchLengthsParameters(), and bpp::AbstractHomogeneousTreeLikelihood::operator=().