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

Inheritance diagram for bpp::RNonHomogeneousMixedTreeLikelihood:

Collaboration diagram for bpp::RNonHomogeneousMixedTreeLikelihood:

Public Member Functions
	RNonHomogeneousMixedTreeLikelihood (const Tree &tree, MixedSubstitutionModelSet modelSet, DiscreteDistribution rDist, bool verbose=true, bool usePatterns=true) throw (Exception)
	Build a new RNonHomogeneousMixeTreeLikelihood object without data.
	RNonHomogeneousMixedTreeLikelihood (const Tree &tree, const SiteContainer &data, MixedSubstitutionModelSet modelSet, DiscreteDistribution rDist, bool verbose=true, bool usePatterns=true) throw (Exception)
	Build a new RNonHomogeneousMixedTreeLikelihood object and compute the corresponding likelihood.
	RNonHomogeneousMixedTreeLikelihood (const RNonHomogeneousMixedTreeLikelihood &lik)
RNonHomogeneousMixedTreeLikelihood &	operator= (const RNonHomogeneousMixedTreeLikelihood &lik)
virtual	~RNonHomogeneousMixedTreeLikelihood ()
RNonHomogeneousMixedTreeLikelihood *	clone () const
void	setParameters (const ParameterList &parameters) throw (ParameterNotFoundException, ConstraintException)
	Implements the Function interface.
double	getValue () const throw (Exception)
DRASRTreeLikelihoodData *	getLikelihoodData ()
const DRASRTreeLikelihoodData *	getLikelihoodData () const
virtual 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 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	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
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 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.
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.
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.
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.
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 SubstitutionModel *	getSubstitutionModelForNode (int nodeId) const throw (NodeNotFoundException)
	Get the substitution model associated to a given node.
SubstitutionModel *	getSubstitutionModelForNode (int nodeId) throw (NodeNotFoundException)
	Get the substitution model associated to a given node.
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 NonHomogeneousTreeLikelihood interface.
Other methods are implemented in the AbstractTreeLikelihood class.
const SubstitutionModelSet *	getSubstitutionModelSet () const
SubstitutionModelSet *	getSubstitutionModelSet ()
void	setSubstitutionModelSet (SubstitutionModelSet *modelSet) throw (Exception)
ParameterList	getRootFrequenciesParameters () const
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	displayLikelihood (const Node *node)
	This method is mainly for debugging purpose.
virtual void	computeAllTransitionProbabilities ()
	Fill the pxy_, dpxy_ and d2pxy_ arrays for all nodes.
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
SubstitutionModelSet *	modelSet_
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.
std::map< int, const Node * >	idToNode_
	An index linking nodes to their id, for faster access than the getNode() method.
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_
bool	reparametrizeRoot_
int	root1_
int	root2_
DiscreteDistribution *	rateDistribution_
const SiteContainer *	data_
TreeTemplate< Node > *	tree_
bool	computeFirstOrderDerivatives_
bool	computeSecondOrderDerivatives_
bool	initialized_
Private Member Functions
	RNonHomogeneousMixedTreeLikelihood (const Tree &tree, MixedSubstitutionModelSet modelSet, const MixedSubstitutionModelSet::HyperNode &hyperNode, int upperNode, DiscreteDistribution rDist, bool verbose, bool usePatterns)
	Build a new RNonHomogeneousMixeTreeLikelihood object without data.
	RNonHomogeneousMixedTreeLikelihood (const Tree &tree, const SiteContainer &data, MixedSubstitutionModelSet modelSet, const MixedSubstitutionModelSet::HyperNode &hyperNode, int upperNode, DiscreteDistribution rDist, bool verbose, bool usePatterns)
	Build a new RNonHomogeneousMixeTreeLikelihood object with data.
void	init (bool usePatterns)
Private Attributes
map< int, vector < RNonHomogeneousMixedTreeLikelihood * > >	mvTreeLikelihoods_
	the map of the branch numbers to the vectors of the TreeLikelihoods for the expanded model on this branch.
MixedSubstitutionModelSet::HyperNode	hyperNode_
	A specific HyperNode in which the computation is processed. If the probability of this HyperNode is -1, it means that it should not be used, and the HyperNodes are all in the MixedSubstitutionModelSet object.
int	upperNode_
	the number of the node under which tree the Treelikelihood is computed.
bool	main_
	a flag to say if this object is the head of the hierarchy
Friends
class	RNonHomogeneousMixedTreeLikelihood
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.
void	initialize () throw (Exception)
	Init the likelihood object.
void	computeTreeDLikelihood (const string &variable)
void	computeTreeD2Likelihood (const string &variable)
double	getProbability () const
	returns the probability of this object in the hierarchy
void	setProbability (double x)
	sets the probability of this object in the hierarchy
const MixedSubstitutionModelSet::HyperNode &	getHyperNode ()
	returns the HyperNode describing the owned submodels.
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)
void	computeTransitionProbabilitiesForNode (const Node *node)
	Fill the pxy_, dpxy_ and d2pxy_ arrays for one node.

Detailed Description

@ brief A class to compute the average of several RNonHomogeneousTreeLikelihood defined from a Mixed Substitution Model.

This class is made recursively. At each node, we test if an expansion of a mixed model is necessary. This is the case when this model points towards different subtrees under this node, or towards a son of this node and a branch under it. If an expansion is necessary, a vector of RNonHomogeneousMixedLikelihood* is built with all the submodels combinations.

Note that this approach is not the most efficient, since a graph based one would avoid some computations, but it seems much more difficult to do it in the extant hierarchy.

Definition at line 69 of file RNonHomogeneousMixedTreeLikelihood.h.

Constructor & Destructor Documentation

RNonHomogeneousMixedTreeLikelihood::RNonHomogeneousMixedTreeLikelihood	(	const Tree &	tree,
		MixedSubstitutionModelSet *	modelSet,
		const MixedSubstitutionModelSet::HyperNode &	hyperNode,
		int	upperNode,
		DiscreteDistribution *	rDist,
		bool	verbose,
		bool	usePatterns
	)		`[private]`

Build a new RNonHomogeneousMixeTreeLikelihood 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.
modelSet	The set of substitution models to use.
hyperNode	an hypernode of the numbers of the submodels used in the mixed models.
upperNode	the number of the node under which the treelikelihood is computed.
rDist	The rate across sites distribution to use. 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 103 of file RNonHomogeneousMixedTreeLikelihood.cpp.

References init(), and bpp::SubstitutionModelSet::isFullySetUpFor().

Referenced by init(), operator=(), and RNonHomogeneousMixedTreeLikelihood().

RNonHomogeneousMixedTreeLikelihood::RNonHomogeneousMixedTreeLikelihood	(	const Tree &	tree,
		const SiteContainer &	data,
		MixedSubstitutionModelSet *	modelSet,
		const MixedSubstitutionModelSet::HyperNode &	hyperNode,
		int	upperNode,
		DiscreteDistribution *	rDist,
		bool	verbose,
		bool	usePatterns
	)		`[private]`

Build a new RNonHomogeneousMixeTreeLikelihood object with 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.
data	Sequences to use.
modelSet	The set of substitution models to use.
hyperNode	an hypernode of the numbers of the submodels used in the mixed models.
upperNode	the number of the node under which the treelikelihood is computed.
rDist	The rate across sites distribution to use. 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 124 of file RNonHomogeneousMixedTreeLikelihood.cpp.

References init(), and bpp::SubstitutionModelSet::isFullySetUpFor().

RNonHomogeneousMixedTreeLikelihood::RNonHomogeneousMixedTreeLikelihood	(	const Tree &	tree,
		MixedSubstitutionModelSet *	modelSet,
		DiscreteDistribution *	rDist,
		bool	verbose = `true`,
		bool	usePatterns = `true`
	)		throw (Exception)

Build a new RNonHomogeneousMixeTreeLikelihood 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.
modelSet	The set of substitution models to use.
rDist	The rate across sites distribution to use. 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 58 of file RNonHomogeneousMixedTreeLikelihood.cpp.

RNonHomogeneousMixedTreeLikelihood::RNonHomogeneousMixedTreeLikelihood	(	const Tree &	tree,
		const SiteContainer &	data,
		MixedSubstitutionModelSet *	modelSet,
		DiscreteDistribution *	rDist,
		bool	verbose = `true`,
		bool	usePatterns = `true`
	)		throw (Exception)

Build a new RNonHomogeneousMixedTreeLikelihood object and compute the corresponding likelihood.

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

Parameters:

tree	The tree to use.
data	Sequences to use.
modelSet	The set of substitution models to use.
rDist	The rate across sites distribution to use.
verbose	Should I display some info?
usePatterns	Tell if recursive site compression should be performed.

Exceptions:

Exception in an error occured.

Definition at line 81 of file RNonHomogeneousMixedTreeLikelihood.cpp.

RNonHomogeneousMixedTreeLikelihood::RNonHomogeneousMixedTreeLikelihood ( const RNonHomogeneousMixedTreeLikelihood & lik )

Definition at line 255 of file RNonHomogeneousMixedTreeLikelihood.cpp.

References mvTreeLikelihoods_, and RNonHomogeneousMixedTreeLikelihood().

RNonHomogeneousMixedTreeLikelihood::~RNonHomogeneousMixedTreeLikelihood ( ) [virtual]

Definition at line 301 of file RNonHomogeneousMixedTreeLikelihood.cpp.

References mvTreeLikelihoods_.

Member Function Documentation

void AbstractNonHomogeneousTreeLikelihood::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.

Definition at line 314 of file AbstractNonHomogeneousTreeLikelihood.cpp.

References bpp::AbstractParametrizable::getParameter(), bpp::AbstractParametrizable::getParameters(), bpp::Parameter::getValue(), bpp::AbstractTreeLikelihood::initialized_, bpp::AbstractParameterAliasable::matchParametersValues(), bpp::DiscreteDistribution::matchParametersValues(), bpp::AbstractNonHomogeneousTreeLikelihood::modelSet_, bpp::AbstractNonHomogeneousTreeLikelihood::nbNodes_, bpp::AbstractNonHomogeneousTreeLikelihood::nodes_, bpp::AbstractDiscreteRatesAcrossSitesTreeLikelihood::rateDistribution_, bpp::AbstractNonHomogeneousTreeLikelihood::reparametrizeRoot_, bpp::AbstractNonHomogeneousTreeLikelihood::root1_, bpp::AbstractNonHomogeneousTreeLikelihood::root2_, and bpp::TextTools::toString().

Referenced by bpp::DRNonHomogeneousTreeLikelihood::fireParameterChanged(), bpp::RNonHomogeneousTreeLikelihood::fireParameterChanged(), and fireParameterChanged().

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

Reimplemented from bpp::RNonHomogeneousTreeLikelihood.

Definition at line 232 of file RNonHomogeneousMixedTreeLikelihood.h.

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

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

Definition at line 393 of file AbstractNonHomogeneousTreeLikelihood.cpp.

References bpp::AbstractNonHomogeneousTreeLikelihood::computeTransitionProbabilitiesForNode(), bpp::SubstitutionModelSet::getRootFrequencies(), bpp::AbstractNonHomogeneousTreeLikelihood::modelSet_, bpp::AbstractNonHomogeneousTreeLikelihood::nbNodes_, bpp::AbstractNonHomogeneousTreeLikelihood::nodes_, and bpp::AbstractNonHomogeneousTreeLikelihood::rootFreqs_.

Referenced by bpp::DRNonHomogeneousTreeLikelihood::fireParameterChanged(), bpp::RNonHomogeneousTreeLikelihood::fireParameterChanged(), fireParameterChanged(), and bpp::AbstractNonHomogeneousTreeLikelihood::initialize().

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

Reimplemented from bpp::RNonHomogeneousTreeLikelihood.

Definition at line 704 of file RNonHomogeneousMixedTreeLikelihood.cpp.

References bpp::Node::getFather(), bpp::Node::getId(), and upperNode_.

Referenced by computeTreeD2Likelihood().

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

Reimplemented from bpp::RNonHomogeneousTreeLikelihood.

Definition at line 611 of file RNonHomogeneousMixedTreeLikelihood.cpp.

References bpp::Node::getFather(), bpp::Node::getId(), and upperNode_.

Referenced by computeTreeDLikelihood().

void RNonHomogeneousMixedTreeLikelihood::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 from bpp::RNonHomogeneousTreeLikelihood.

Definition at line 465 of file RNonHomogeneousMixedTreeLikelihood.cpp.

References bpp::Node::getId(), bpp::DRASRTreeLikelihoodData::getLikelihoodArray(), getProbability(), bpp::Node::isLeaf(), bpp::RNonHomogeneousTreeLikelihood::likelihoodData_, main_, mvTreeLikelihoods_, bpp::AbstractNonHomogeneousTreeLikelihood::nbClasses_, bpp::AbstractNonHomogeneousTreeLikelihood::nbStates_, and upperNode_.

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

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

Reimplemented from bpp::AbstractNonHomogeneousTreeLikelihood.

Definition at line 721 of file RNonHomogeneousMixedTreeLikelihood.cpp.

References bpp::AbstractTreeLikelihood::computeFirstOrderDerivatives_, bpp::AbstractTreeLikelihood::computeSecondOrderDerivatives_, bpp::AbstractNonHomogeneousTreeLikelihood::d2pxy_, bpp::AbstractNonHomogeneousTreeLikelihood::dpxy_, bpp::DiscreteDistribution::getCategory(), bpp::Node::getDistanceToFather(), bpp::Node::getId(), bpp::SubstitutionModelSet::getModelForNode(), bpp::SubstitutionModelSet::getModelIndexForNode(), bpp::MixedSubstitutionModel::getNModel(), bpp::MixedSubstitutionModelSet::HyperNode::getNode(), bpp::MixedSubstitutionModel::getNProbability(), hyperNode_, bpp::AbstractNonHomogeneousTreeLikelihood::modelSet_, bpp::AbstractNonHomogeneousTreeLikelihood::nbClasses_, bpp::AbstractNonHomogeneousTreeLikelihood::nbStates_, bpp::AbstractNonHomogeneousTreeLikelihood::pxy_, bpp::AbstractDiscreteRatesAcrossSitesTreeLikelihood::rateDistribution_, and bpp::MixedSubstitutionModelSet::HyperNode::Node::size().

Referenced by fireParameterChanged().

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

Reimplemented from bpp::RNonHomogeneousTreeLikelihood.

Definition at line 628 of file RNonHomogeneousMixedTreeLikelihood.cpp.

References computeDownSubtreeD2Likelihood(), bpp::DRASRTreeLikelihoodData::getD2LikelihoodArray(), bpp::Node::getFather(), bpp::Node::getId(), getProbability(), bpp::TreeTemplate< N >::getRootNode(), bpp::RNonHomogeneousTreeLikelihood::likelihoodData_, main_, mvTreeLikelihoods_, bpp::AbstractNonHomogeneousTreeLikelihood::nbClasses_, bpp::AbstractNonHomogeneousTreeLikelihood::nbStates_, bpp::AbstractNonHomogeneousTreeLikelihood::nodes_, bpp::AbstractTreeLikelihood::tree_, and upperNode_.

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

Reimplemented from bpp::RNonHomogeneousTreeLikelihood.

Definition at line 537 of file RNonHomogeneousMixedTreeLikelihood.cpp.

References computeDownSubtreeDLikelihood(), bpp::DRASRTreeLikelihoodData::getDLikelihoodArray(), bpp::Node::getFather(), bpp::Node::getId(), getProbability(), bpp::TreeTemplate< N >::getRootNode(), bpp::RNonHomogeneousTreeLikelihood::likelihoodData_, main_, mvTreeLikelihoods_, bpp::AbstractNonHomogeneousTreeLikelihood::nbClasses_, bpp::AbstractNonHomogeneousTreeLikelihood::nbStates_, bpp::AbstractNonHomogeneousTreeLikelihood::nodes_, bpp::AbstractTreeLikelihood::tree_, and upperNode_.

void RNonHomogeneousTreeLikelihood::computeTreeLikelihood ( ) [virtual, inherited]

Definition at line 1285 of file RNonHomogeneousTreeLikelihood.cpp.

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

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

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

This method is mainly for debugging purpose.

Parameters:

node	The node at which likelihood values must be displayed.

Definition at line 1359 of file RNonHomogeneousTreeLikelihood.cpp.

References bpp::AbstractDiscreteRatesAcrossSitesTreeLikelihood::displayLikelihoodArray(), bpp::Node::getId(), bpp::DRASRTreeLikelihoodData::getLikelihoodArray(), bpp::Node::getName(), and bpp::RNonHomogeneousTreeLikelihood::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(), 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 RNonHomogeneousMixedTreeLikelihood::fireParameterChanged ( const ParameterList & params ) [protected, virtual]

Reimplemented from bpp::RNonHomogeneousTreeLikelihood.

Definition at line 337 of file RNonHomogeneousMixedTreeLikelihood.cpp.

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 AbstractNonHomogeneousTreeLikelihood::getBranchLengthsParameters ( ) const [virtual, inherited]

Get the branch lengths parameters.

Returns:: A ParameterList with all branch lengths.

Implements bpp::TreeLikelihood.

Definition at line 280 of file AbstractNonHomogeneousTreeLikelihood.cpp.

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

double RNonHomogeneousTreeLikelihood::getD2LikelihoodForASite ( size_t site ) const [virtual, inherited]

Definition at line 814 of file RNonHomogeneousTreeLikelihood.cpp.

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

Referenced by bpp::RNonHomogeneousTreeLikelihood::getD2LogLikelihoodForASite().

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

Definition at line 799 of file RNonHomogeneousTreeLikelihood.cpp.

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

Referenced by bpp::RNonHomogeneousTreeLikelihood::getD2LikelihoodForASite().

double RNonHomogeneousTreeLikelihood::getD2LogLikelihood ( ) const [virtual, inherited]

Definition at line 835 of file RNonHomogeneousTreeLikelihood.cpp.

References bpp::RNonHomogeneousTreeLikelihood::getD2LogLikelihoodForASite(), and bpp::AbstractNonHomogeneousTreeLikelihood::nbSites_.

double RNonHomogeneousTreeLikelihood::getD2LogLikelihoodForASite ( size_t site ) const [virtual, inherited]

Definition at line 827 of file RNonHomogeneousTreeLikelihood.cpp.

References bpp::RNonHomogeneousTreeLikelihood::getD2LikelihoodForASite(), bpp::RNonHomogeneousTreeLikelihood::getDLikelihoodForASite(), and bpp::RNonHomogeneousTreeLikelihood::getLikelihoodForASite().

Referenced by bpp::RNonHomogeneousTreeLikelihood::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 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 RNonHomogeneousTreeLikelihood::getDLikelihoodForASite ( size_t site ) const [virtual, inherited]

Definition at line 342 of file RNonHomogeneousTreeLikelihood.cpp.

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

Referenced by bpp::RNonHomogeneousTreeLikelihood::getD2LogLikelihoodForASite(), and bpp::RNonHomogeneousTreeLikelihood::getDLogLikelihoodForASite().

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

Definition at line 327 of file RNonHomogeneousTreeLikelihood.cpp.

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

Referenced by bpp::RNonHomogeneousTreeLikelihood::getDLikelihoodForASite().

double RNonHomogeneousTreeLikelihood::getDLogLikelihood ( ) const [virtual, inherited]

Definition at line 363 of file RNonHomogeneousTreeLikelihood.cpp.

References bpp::RNonHomogeneousTreeLikelihood::getDLogLikelihoodForASite(), and bpp::AbstractNonHomogeneousTreeLikelihood::nbSites_.

double RNonHomogeneousTreeLikelihood::getDLogLikelihoodForASite ( size_t site ) const [virtual, inherited]

Definition at line 355 of file RNonHomogeneousTreeLikelihood.cpp.

References bpp::RNonHomogeneousTreeLikelihood::getDLikelihoodForASite(), and bpp::RNonHomogeneousTreeLikelihood::getLikelihoodForASite().

Referenced by bpp::RNonHomogeneousTreeLikelihood::getDLogLikelihood().

double RNonHomogeneousTreeLikelihood::getFirstOrderDerivative ( const std::string & variable ) const throw (Exception) [virtual, inherited]

Implements bpp::DerivableSecondOrder.

Definition at line 376 of file RNonHomogeneousTreeLikelihood.cpp.

const MixedSubstitutionModelSet::HyperNode& bpp::RNonHomogeneousMixedTreeLikelihood::getHyperNode ( ) [inline]

returns the HyperNode describing the owned submodels.

Definition at line 271 of file RNonHomogeneousMixedTreeLikelihood.h.

double RNonHomogeneousTreeLikelihood::getLikelihood ( ) const [virtual, inherited]

Get the likelihood for the whole dataset.

Returns:: The likelihood of the dataset.

Implements bpp::TreeLikelihood.

Definition at line 158 of file RNonHomogeneousTreeLikelihood.cpp.

References bpp::RNonHomogeneousTreeLikelihood::getLikelihoodForASite(), and bpp::AbstractNonHomogeneousTreeLikelihood::nbSites_.

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

Returns:: The underlying likelihood data structure.

Implements bpp::TreeLikelihood.

Definition at line 222 of file RNonHomogeneousTreeLikelihood.h.

References bpp::RNonHomogeneousTreeLikelihood::likelihoodData_.

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

Returns:: The underlying likelihood data structure.

Implements bpp::TreeLikelihood.

Definition at line 223 of file RNonHomogeneousTreeLikelihood.h.

References bpp::RNonHomogeneousTreeLikelihood::likelihoodData_.

double RNonHomogeneousTreeLikelihood::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 188 of file RNonHomogeneousTreeLikelihood.cpp.

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

Referenced by bpp::RNonHomogeneousTreeLikelihood::getD2LogLikelihoodForASite(), bpp::RNonHomogeneousTreeLikelihood::getDLogLikelihoodForASite(), and bpp::RNonHomogeneousTreeLikelihood::getLikelihood().

double RNonHomogeneousTreeLikelihood::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 214 of file RNonHomogeneousTreeLikelihood.cpp.

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

Referenced by bpp::RNonHomogeneousTreeLikelihood::getLikelihoodForASite(), and bpp::RNonHomogeneousTreeLikelihood::getLogLikelihoodForASite().

double RNonHomogeneousTreeLikelihood::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 240 of file RNonHomogeneousTreeLikelihood.cpp.

References bpp::Node::getId(), bpp::DRASRTreeLikelihoodData::getLikelihoodArray(), bpp::DRASRTreeLikelihoodData::getRootArrayPosition(), bpp::TreeTemplate< N >::getRootNode(), bpp::RNonHomogeneousTreeLikelihood::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 RNonHomogeneousTreeLikelihood::getLogLikelihood ( ) const [virtual, inherited]

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 170 of file RNonHomogeneousTreeLikelihood.cpp.

References bpp::RNonHomogeneousTreeLikelihood::getLogLikelihoodForASite(), and bpp::AbstractNonHomogeneousTreeLikelihood::nbSites_.

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

double RNonHomogeneousTreeLikelihood::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 200 of file RNonHomogeneousTreeLikelihood.cpp.

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

Referenced by bpp::RNonHomogeneousTreeLikelihood::getLogLikelihood().

double RNonHomogeneousTreeLikelihood::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 227 of file RNonHomogeneousTreeLikelihood.cpp.

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

double RNonHomogeneousTreeLikelihood::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 247 of file RNonHomogeneousTreeLikelihood.cpp.

References bpp::Node::getId(), bpp::DRASRTreeLikelihoodData::getLikelihoodArray(), bpp::DRASRTreeLikelihoodData::getRootArrayPosition(), bpp::TreeTemplate< N >::getRootNode(), bpp::RNonHomogeneousTreeLikelihood::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::AbstractNonHomogeneousTreeLikelihood::getMaximumBranchLength ( ) const [inline, virtual, inherited]

Definition at line 271 of file AbstractNonHomogeneousTreeLikelihood.h.

References bpp::AbstractNonHomogeneousTreeLikelihood::maximumBrLen_.

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

Definition at line 270 of file AbstractNonHomogeneousTreeLikelihood.h.

References bpp::AbstractNonHomogeneousTreeLikelihood::minimumBrLen_.

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

Implements bpp::TreeLikelihood.

Definition at line 202 of file AbstractNonHomogeneousTreeLikelihood.h.

References bpp::SubstitutionModelSet::getModelForNode(), bpp::AbstractNonHomogeneousTreeLikelihood::modelSet_, and bpp::AbstractNonHomogeneousTreeLikelihood::nbDistinctSites_.

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

Implements bpp::TreeLikelihood.

Definition at line 207 of file AbstractNonHomogeneousTreeLikelihood.h.

References bpp::AbstractNonHomogeneousTreeLikelihood::modelSet_.

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.

double RNonHomogeneousMixedTreeLikelihood::getProbability ( ) const

returns the probability of this object in the hierarchy

Definition at line 452 of file RNonHomogeneousMixedTreeLikelihood.cpp.

References bpp::MixedSubstitutionModelSet::HyperNode::getProbability(), and hyperNode_.

Referenced by computeSubtreeLikelihood(), computeTreeD2Likelihood(), and computeTreeDLikelihood().

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::AbstractNonHomogeneousTreeLikelihood::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 183 of file AbstractNonHomogeneousTreeLikelihood.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::AbstractNonHomogeneousTreeLikelihood::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 198 of file AbstractNonHomogeneousTreeLikelihood.h.

References bpp::AbstractNonHomogeneousTreeLikelihood::rootFreqs_.

ParameterList bpp::AbstractNonHomogeneousTreeLikelihood::getRootFrequenciesParameters ( ) const [inline, virtual, inherited]

Returns:: The parameters on which the root frequencies depend.

Implements bpp::NonHomogeneousTreeLikelihood.

Definition at line 227 of file AbstractNonHomogeneousTreeLikelihood.h.

References bpp::SubstitutionModelSet::getRootFrequenciesParameters(), and bpp::AbstractNonHomogeneousTreeLikelihood::modelSet_.

double RNonHomogeneousTreeLikelihood::getSecondOrderDerivative ( const std::string & variable ) const throw (Exception) [virtual, inherited]

Implements bpp::DerivableSecondOrder.

Definition at line 848 of file RNonHomogeneousTreeLikelihood.cpp.

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

Implements bpp::DerivableSecondOrder.

Definition at line 217 of file RNonHomogeneousTreeLikelihood.h.

size_t bpp::RNonHomogeneousTreeLikelihood::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 172 of file RNonHomogeneousTreeLikelihood.h.

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

const SubstitutionModel* bpp::NonHomogeneousTreeLikelihood::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 69 of file NonHomogeneousTreeLikelihood.h.

References bpp::NonHomogeneousTreeLikelihood::getSubstitutionModelForNode().

SubstitutionModel* bpp::NonHomogeneousTreeLikelihood::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 74 of file NonHomogeneousTreeLikelihood.h.

References bpp::NonHomogeneousTreeLikelihood::getSubstitutionModelForNode().

const SubstitutionModel* bpp::AbstractNonHomogeneousTreeLikelihood::getSubstitutionModelForNode ( int nodeId ) const throw (NodeNotFoundException) [inline, virtual, inherited]

Get the substitution model associated to a given node.

Parameters:

nodeId The id of the request node.

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::NonHomogeneousTreeLikelihood.

Definition at line 188 of file AbstractNonHomogeneousTreeLikelihood.h.

References bpp::SubstitutionModelSet::getModelForNode(), and bpp::AbstractNonHomogeneousTreeLikelihood::modelSet_.

SubstitutionModel* bpp::AbstractNonHomogeneousTreeLikelihood::getSubstitutionModelForNode ( int nodeId ) throw (NodeNotFoundException) [inline, virtual, inherited]

Get the substitution model associated to a given node.

Parameters:

nodeId The id of the request node.

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::NonHomogeneousTreeLikelihood.

Definition at line 193 of file AbstractNonHomogeneousTreeLikelihood.h.

References bpp::SubstitutionModelSet::getModelForNode(), and bpp::AbstractNonHomogeneousTreeLikelihood::modelSet_.

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

Get the parameters associated to substitution model(s).

Returns:: A ParameterList.

Implements bpp::TreeLikelihood.

Definition at line 288 of file AbstractNonHomogeneousTreeLikelihood.cpp.

References bpp::ParameterList::getCommonParametersWith(), bpp::AbstractParametrizable::getParameters(), bpp::AbstractParameterAliasable::getParameters(), bpp::AbstractTreeLikelihood::initialized_, and bpp::AbstractNonHomogeneousTreeLikelihood::modelSet_.

const SubstitutionModelSet* bpp::AbstractNonHomogeneousTreeLikelihood::getSubstitutionModelSet ( ) const [inline, virtual, inherited]

Returns:: The set of substitution models associated to this instance.

Implements bpp::NonHomogeneousTreeLikelihood.

Definition at line 221 of file AbstractNonHomogeneousTreeLikelihood.h.

References bpp::AbstractNonHomogeneousTreeLikelihood::modelSet_.

SubstitutionModelSet* bpp::AbstractNonHomogeneousTreeLikelihood::getSubstitutionModelSet ( ) [inline, virtual, inherited]

Returns:: The set of substitution models associated to this instance.

Implements bpp::NonHomogeneousTreeLikelihood.

Definition at line 223 of file AbstractNonHomogeneousTreeLikelihood.h.

References bpp::AbstractNonHomogeneousTreeLikelihood::modelSet_.

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::AbstractNonHomogeneousTreeLikelihood::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 200 of file AbstractNonHomogeneousTreeLikelihood.h.

References bpp::AbstractNonHomogeneousTreeLikelihood::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 init().

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

Implements bpp::DerivableSecondOrder.

Definition at line 316 of file RNonHomogeneousTreeLikelihood.cpp.

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

void RNonHomogeneousMixedTreeLikelihood::init ( bool usePatterns ) [private]

brief method where the recursive structure is built.

Definition at line 146 of file RNonHomogeneousMixedTreeLikelihood.cpp.

References bpp::AbstractTreeLikelihood::getData(), bpp::MixedSubstitutionModelSet::HyperNode::getNode(), bpp::TreeTools::getNodesId(), bpp::SubstitutionModelSet::getNodesWithModel(), bpp::SubstitutionModelSet::getNumberOfModels(), bpp::Tree::getSonsId(), bpp::AbstractTreeLikelihood::getTree(), hyperNode_, bpp::AbstractNonHomogeneousTreeLikelihood::modelSet_, mvTreeLikelihoods_, bpp::AbstractDiscreteRatesAcrossSitesTreeLikelihood::rateDistribution_, bpp::AbstractParametrizable::resetParameters_(), RNonHomogeneousMixedTreeLikelihood(), bpp::MixedSubstitutionModelSet::HyperNode::setModel(), bpp::MixedSubstitutionModelSet::HyperNode::setProbability(), bpp::MixedSubstitutionModelSet::HyperNode::Node::size(), and upperNode_.

Referenced by RNonHomogeneousMixedTreeLikelihood().

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

Definition at line 348 of file AbstractNonHomogeneousTreeLikelihood.cpp.

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

void RNonHomogeneousMixedTreeLikelihood::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::AbstractNonHomogeneousTreeLikelihood.

Definition at line 314 of file RNonHomogeneousMixedTreeLikelihood.cpp.

References bpp::AbstractParametrizable::addParameters_(), bpp::AbstractNonHomogeneousTreeLikelihood::brLenParameters_, bpp::AbstractNonHomogeneousTreeLikelihood::initBranchLengthsParameters(), bpp::AbstractNonHomogeneousTreeLikelihood::initParameters(), main_, and mvTreeLikelihoods_.

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

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

Definition at line 296 of file AbstractNonHomogeneousTreeLikelihood.cpp.

References bpp::AbstractParametrizable::addParameters_(), bpp::AbstractNonHomogeneousTreeLikelihood::brLenParameters_, bpp::DiscreteDistribution::getIndependentParameters(), bpp::AbstractParameterAliasable::getIndependentParameters(), bpp::AbstractNonHomogeneousTreeLikelihood::initBranchLengthsParameters(), bpp::AbstractNonHomogeneousTreeLikelihood::modelSet_, bpp::AbstractDiscreteRatesAcrossSitesTreeLikelihood::rateDistribution_, and bpp::AbstractParametrizable::resetParameters_().

Referenced by bpp::AbstractNonHomogeneousTreeLikelihood::initialize(), and 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().

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

Definition at line 275 of file RNonHomogeneousMixedTreeLikelihood.cpp.

References hyperNode_, main_, mvTreeLikelihoods_, RNonHomogeneousMixedTreeLikelihood(), and upperNode_.

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 RNonHomogeneousMixedTreeLikelihood::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::RNonHomogeneousTreeLikelihood.

Definition at line 437 of file RNonHomogeneousMixedTreeLikelihood.cpp.

References bpp::RNonHomogeneousTreeLikelihood::setData().

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

Definition at line 260 of file AbstractNonHomogeneousTreeLikelihood.h.

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

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

Definition at line 250 of file AbstractNonHomogeneousTreeLikelihood.h.

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

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

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 254 of file RNonHomogeneousTreeLikelihood.cpp.

void RNonHomogeneousMixedTreeLikelihood::setProbability ( double x )

sets the probability of this object in the hierarchy

Definition at line 458 of file RNonHomogeneousMixedTreeLikelihood.cpp.

References hyperNode_, and bpp::MixedSubstitutionModelSet::HyperNode::setProbability().

Referenced by fireParameterChanged().

void AbstractNonHomogeneousTreeLikelihood::setSubstitutionModelSet ( SubstitutionModelSet * model ) throw (Exception) [virtual, inherited]

Returns:: Set the substitution models for this instance.

Exceptions:

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

Implements bpp::NonHomogeneousTreeLikelihood.

Definition at line 195 of file AbstractNonHomogeneousTreeLikelihood.cpp.

References bpp::Node::getId().

Friends And Related Function Documentation

friend class RNonHomogeneousMixedTreeLikelihood [friend, inherited]

Definition at line 271 of file RNonHomogeneousTreeLikelihood.h.

Member Data Documentation

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

Definition at line 127 of file AbstractNonHomogeneousTreeLikelihood.h.

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

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

Definition at line 93 of file AbstractNonHomogeneousTreeLikelihood.h.

Referenced by bpp::DRNonHomogeneousTreeLikelihood::fireParameterChanged(), bpp::RNonHomogeneousTreeLikelihood::fireParameterChanged(), fireParameterChanged(), bpp::AbstractNonHomogeneousTreeLikelihood::getBranchLengthsParameters(), bpp::AbstractNonHomogeneousTreeLikelihood::initBranchLengthsParameters(), initialize(), bpp::AbstractNonHomogeneousTreeLikelihood::initParameters(), and bpp::AbstractNonHomogeneousTreeLikelihood::operator=().

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

Definition at line 227 of file AbstractTreeLikelihood.h.

Referenced by bpp::AbstractHomogeneousTreeLikelihood::computeTransitionProbabilitiesForNode(), bpp::AbstractNonHomogeneousTreeLikelihood::computeTransitionProbabilitiesForNode(), 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(), 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::AbstractNonHomogeneousTreeLikelihood::d2pxy_ [mutable, protected, inherited]

Definition at line 99 of file AbstractNonHomogeneousTreeLikelihood.h.

Referenced by bpp::AbstractNonHomogeneousTreeLikelihood::computeTransitionProbabilitiesForNode(), computeTransitionProbabilitiesForNode(), bpp::RNonHomogeneousTreeLikelihood::computeTreeD2Likelihood(), bpp::DRNonHomogeneousTreeLikelihood::computeTreeD2LikelihoodAtNode(), and bpp::AbstractNonHomogeneousTreeLikelihood::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::AbstractNonHomogeneousTreeLikelihood::dpxy_ [mutable, protected, inherited]

Definition at line 97 of file AbstractNonHomogeneousTreeLikelihood.h.

Referenced by bpp::AbstractNonHomogeneousTreeLikelihood::computeTransitionProbabilitiesForNode(), computeTransitionProbabilitiesForNode(), bpp::RNonHomogeneousTreeLikelihood::computeTreeD2Likelihood(), bpp::RNonHomogeneousTreeLikelihood::computeTreeDLikelihood(), bpp::DRNonHomogeneousTreeLikelihood::computeTreeDLikelihoodAtNode(), and bpp::AbstractNonHomogeneousTreeLikelihood::operator=().

MixedSubstitutionModelSet::HyperNode bpp::RNonHomogeneousMixedTreeLikelihood::hyperNode_ [private]

A specific HyperNode in which the computation is processed. If the probability of this HyperNode is -1, it means that it should not be used, and the HyperNodes are all in the MixedSubstitutionModelSet object.

This object owns the HyperNode pointers of the owned RNonHomogeneousMixedTreeLikelihood.

Definition at line 92 of file RNonHomogeneousMixedTreeLikelihood.h.

Referenced by computeTransitionProbabilitiesForNode(), getProbability(), init(), operator=(), and setProbability().

std::map<int, const Node*> bpp::AbstractNonHomogeneousTreeLikelihood::idToNode_ [mutable, protected, inherited]

An index linking nodes to their id, for faster access than the getNode() method.

Definition at line 114 of file AbstractNonHomogeneousTreeLikelihood.h.

Referenced by bpp::AbstractNonHomogeneousTreeLikelihood::AbstractNonHomogeneousTreeLikelihood(), bpp::DRNonHomogeneousTreeLikelihood::fireParameterChanged(), bpp::RNonHomogeneousTreeLikelihood::fireParameterChanged(), fireParameterChanged(), and bpp::AbstractNonHomogeneousTreeLikelihood::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=().

bool bpp::RNonHomogeneousMixedTreeLikelihood::main_ [private]

a flag to say if this object is the head of the hierarchy

Definition at line 107 of file RNonHomogeneousMixedTreeLikelihood.h.

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

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

Definition at line 126 of file AbstractNonHomogeneousTreeLikelihood.h.

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

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

Definition at line 125 of file AbstractNonHomogeneousTreeLikelihood.h.

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

SubstitutionModelSet* bpp::AbstractNonHomogeneousTreeLikelihood::modelSet_ [protected, inherited]

Definition at line 92 of file AbstractNonHomogeneousTreeLikelihood.h.

map<int, vector<RNonHomogeneousMixedTreeLikelihood*> > bpp::RNonHomogeneousMixedTreeLikelihood::mvTreeLikelihoods_ [private]

the map of the branch numbers to the vectors of the TreeLikelihoods for the expanded model on this branch.

Definition at line 80 of file RNonHomogeneousMixedTreeLikelihood.h.

Referenced by computeSubtreeLikelihood(), computeTreeD2Likelihood(), computeTreeDLikelihood(), fireParameterChanged(), init(), initialize(), operator=(), RNonHomogeneousMixedTreeLikelihood(), and ~RNonHomogeneousMixedTreeLikelihood().

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

Definition at line 117 of file AbstractNonHomogeneousTreeLikelihood.h.

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

Definition at line 117 of file AbstractNonHomogeneousTreeLikelihood.h.

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

Definition at line 117 of file AbstractNonHomogeneousTreeLikelihood.h.

Referenced by bpp::AbstractNonHomogeneousTreeLikelihood::applyParameters(), bpp::AbstractNonHomogeneousTreeLikelihood::computeAllTransitionProbabilities(), bpp::DRNonHomogeneousTreeLikelihood::computeTreeD2Likelihoods(), bpp::DRNonHomogeneousTreeLikelihood::computeTreeDLikelihoods(), fireParameterChanged(), bpp::AbstractNonHomogeneousTreeLikelihood::initBranchLengthsParameters(), and bpp::AbstractNonHomogeneousTreeLikelihood::operator=().

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

Definition at line 117 of file AbstractNonHomogeneousTreeLikelihood.h.

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

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

Definition at line 117 of file AbstractNonHomogeneousTreeLikelihood.h.

std::vector<Node*> bpp::AbstractNonHomogeneousTreeLikelihood::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 109 of file AbstractNonHomogeneousTreeLikelihood.h.