Partial implementation for branch non-homogeneous models of the TreeLikelihood interface. More...

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

Inheritance diagram for bpp::AbstractNonHomogeneousTreeLikelihood:

Collaboration diagram for bpp::AbstractNonHomogeneousTreeLikelihood:

Classes
class	ConstNonHomogeneousSiteModelIterator
Public Member Functions
	AbstractNonHomogeneousTreeLikelihood (const Tree &tree, SubstitutionModelSet modelSet, DiscreteDistribution rDist, bool verbose=true, bool reparametrizeRoot=true) throw (Exception)
	AbstractNonHomogeneousTreeLikelihood (const AbstractNonHomogeneousTreeLikelihood &lik)
	Copy constructor.
AbstractNonHomogeneousTreeLikelihood &	operator= (const AbstractNonHomogeneousTreeLikelihood &lik)
	Assignation operator.
virtual	~AbstractNonHomogeneousTreeLikelihood ()
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
NonHomogeneousTreeLikelihood *	clone () const =0
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	setData (const SiteContainer &sites)=0
	Set the dataset for which the likelihood must be evaluated.
virtual const SiteContainer *	getData () const =0
	Get the dataset for which the likelihood must be evaluated.
virtual bool	isInitialized () const =0
virtual TreeLikelihoodData *	getLikelihoodData ()=0
virtual const TreeLikelihoodData *	getLikelihoodData () const =0
virtual double	getLikelihoodForASite (size_t site) const =0
	Get the likelihood for a site.
virtual double	getLogLikelihoodForASite (size_t site) const =0
	Get the logarithm of the likelihood for a site.
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 double	getLikelihood () const =0
	Get the likelihood for the whole dataset.
virtual double	getLogLikelihood () const =0
	Get the logarithm of the likelihood for the whole dataset.
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	getSecondOrderDerivative (const std::string &variable) const =0
virtual double	getSecondOrderDerivative (const std::string &variable1, const std::string &variable2) 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	getFirstOrderDerivative (const std::string &variable) const =0
virtual double	df (const std::string &variable, const ParameterList &parameters)
virtual void	setParameters (const ParameterList &parameters)=0
virtual double	getValue () const =0
virtual double	f (const ParameterList &parameters)
virtual bool	hasParameter (const std::string &name) const =0
virtual const ParameterList &	getParameters () const =0
virtual const Parameter &	getParameter (const std::string &name) const =0
virtual double	getParameterValue (const std::string &name) const =0
virtual void	setAllParametersValues (const ParameterList &parameters)=0
virtual void	setParameterValue (const std::string &name, double value)=0
virtual void	setParametersValues (const ParameterList &parameters)=0
virtual bool	matchParametersValues (const ParameterList &parameters)=0
virtual size_t	getNumberOfParameters () const =0
virtual void	setNamespace (const std::string &prefix)=0
virtual std::string	getNamespace () const =0
virtual std::string	getParameterNameWithoutNamespace (const std::string &name) const =0
virtual Clonable *	clone () const =0
bool	hasParameter (const std::string &name) const
const ParameterList &	getParameters () const
const Parameter &	getParameter (const std::string &name) const
double	getParameterValue (const std::string &name) const
void	setAllParametersValues (const ParameterList &parameters)
void	setParameterValue (const std::string &name, double value)
void	setParametersValues (const ParameterList &parameters)
bool	matchParametersValues (const ParameterList &parameters)
size_t	getNumberOfParameters () const
void	setNamespace (const std::string &prefix)
std::string	getNamespace () const
std::string	getParameterNameWithoutNamespace (const std::string &name) const
virtual void	fireParameterChanged (const ParameterList &parameters)=0
virtual double	getLikelihoodForASiteForARateClass (size_t site, size_t rateClass) const =0
	Get the likelihood for a site knowing its rate class.
virtual double	getLogLikelihoodForASiteForARateClass (size_t site, size_t rateClass) const =0
	Get the logarithm of the likelihood for a site knowing its rate class.
virtual double	getLikelihoodForASiteForARateClassForAState (size_t site, size_t rateClass, int state) const =0
	Get the likelihood for a site knowing its rate class and its ancestral state.
virtual double	getLogLikelihoodForASiteForARateClassForAState (size_t site, size_t rateClass, int state) const =0
	Get the logarithm of the likelihood for a site knowing its rate class and its ancestral state.
The TreeLikelihood interface.
Other methods are implemented in the AbstractTreeLikelihood class.
void	initialize () throw (Exception)
	Init the likelihood object.
ParameterList	getBranchLengthsParameters () const
	Get the branch lengths parameters.
ParameterList	getSubstitutionModelParameters () const
	Get the parameters associated to substitution model(s).
ParameterList	getRateDistributionParameters () const
	Get the parameters associated to the rate distirbution.
const 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
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.
virtual size_t	getSiteIndex (size_t site) const =0 throw (IndexOutOfBoundsException)
	Get the index (used for inner computations) of a given site (original alignment column).
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.
ParameterList	getDerivableParameters () const
	All derivable parameters.
ParameterList	getNonDerivableParameters () const
	All non derivable parameters.
VVdouble	getTransitionProbabilities (int nodeId, size_t siteIndex) const
	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.
The TreeLikelihood interface.
const SiteContainer *	getData () const
	Get the dataset for which the likelihood must be evaluated.
const Alphabet *	getAlphabet () const
	Get the alphabet associated to the dataset.
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.
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 Tree &	getTree () const
	Get the tree (topology and branch lengths).
void	enableDerivatives (bool yn)
	Tell if derivatives must be computed.
void	enableFirstOrderDerivatives (bool yn)
bool	enableFirstOrderDerivatives () const
void	enableSecondOrderDerivatives (bool yn)
bool	enableSecondOrderDerivatives () const
bool	isInitialized () const
Static Public Member Functions
Generic tools to deal with likelihood arrays
static void	resetLikelihoodArray (VVVdouble &likelihoodArray)
	Set all conditional likelihoods to 1.
static void	displayLikelihoodArray (const VVVdouble &likelihoodArray)
	Print the likelihood array to terminal (debugging tool).
Protected Member Functions
virtual void	computeAllTransitionProbabilities ()
	Fill the pxy_, dpxy_ and d2pxy_ arrays for all nodes.
virtual void	computeTransitionProbabilitiesForNode (const Node *node)
	Fill the pxy_, dpxy_ and d2pxy_ arrays for one node.
void	addParameter_ (Parameter *parameter)
void	addParameters_ (const ParameterList &parameters)
void	deleteParameter_ (size_t index)
void	resetParameters_ ()
Parameter &	getParameter_ (const std::string &name)
Parameter &	getParameter_ (size_t index)
const Parameter &	getParameter_ (size_t index) const
Parameter &	getParameterWithNamespace_ (const std::string &name)
const Parameter &	getParameterWithNamespace_ (const std::string &name) const
ParameterList &	getParameters_ ()
Protected Attributes
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
void	init_ (const Tree &tree, SubstitutionModelSet modelSet, DiscreteDistribution rDist, bool verbose) throw (Exception)
	Method called by constructor.

Detailed Description

Partial implementation for branch non-homogeneous models of the TreeLikelihood interface.

This class provides a pointer toward a single substitution model + several utilitary variables.

Definition at line 58 of file AbstractNonHomogeneousTreeLikelihood.h.

Constructor & Destructor Documentation

AbstractNonHomogeneousTreeLikelihood::AbstractNonHomogeneousTreeLikelihood	(	const Tree &	tree,
		SubstitutionModelSet *	modelSet,
		DiscreteDistribution *	rDist,
		bool	verbose = `true`,
		bool	reparametrizeRoot = `true`
	)		throw (Exception)

Definition at line 58 of file AbstractNonHomogeneousTreeLikelihood.cpp.

AbstractNonHomogeneousTreeLikelihood::AbstractNonHomogeneousTreeLikelihood ( const AbstractNonHomogeneousTreeLikelihood & lik )

Copy constructor.

This constructor is to be called by the derived class copy constructor.

Definition at line 92 of file AbstractNonHomogeneousTreeLikelihood.cpp.

References bpp::Node::getId(), bpp::TreeTemplate< N >::getNodes(), idToNode_, nodes_, and bpp::AbstractTreeLikelihood::tree_.

virtual bpp::AbstractNonHomogeneousTreeLikelihood::~AbstractNonHomogeneousTreeLikelihood ( ) [inline, virtual]

Definition at line 155 of file AbstractNonHomogeneousTreeLikelihood.h.

Member Function Documentation

void AbstractNonHomogeneousTreeLikelihood::applyParameters ( ) throw (Exception) [virtual]

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(), modelSet_, nbNodes_, nodes_, bpp::AbstractDiscreteRatesAcrossSitesTreeLikelihood::rateDistribution_, reparametrizeRoot_, root1_, root2_, and bpp::TextTools::toString().

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

NonHomogeneousTreeLikelihood* bpp::NonHomogeneousTreeLikelihood::clone ( ) const [pure virtual, inherited]

Implements bpp::TreeLikelihood.

Implemented in bpp::RNonHomogeneousMixedTreeLikelihood, bpp::RNonHomogeneousTreeLikelihood, and bpp::DRNonHomogeneousTreeLikelihood.

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

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

Definition at line 393 of file AbstractNonHomogeneousTreeLikelihood.cpp.

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

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

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

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

Reimplemented in bpp::RNonHomogeneousMixedTreeLikelihood.

Definition at line 406 of file AbstractNonHomogeneousTreeLikelihood.cpp.

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

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

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_.

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]

Get the branch lengths parameters.

Returns:: A ParameterList with all branch lengths.

Implements bpp::TreeLikelihood.

Definition at line 280 of file AbstractNonHomogeneousTreeLikelihood.cpp.

References 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.

virtual double bpp::TreeLikelihood::getLikelihood ( ) const [pure virtual, inherited]

Get the likelihood for the whole dataset.

Returns:: The likelihood of the dataset.

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

virtual TreeLikelihoodData* bpp::TreeLikelihood::getLikelihoodData ( ) [pure virtual, inherited]

Returns:: The underlying likelihood data structure.

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

virtual const TreeLikelihoodData* bpp::TreeLikelihood::getLikelihoodData ( ) const [pure virtual, inherited]

Returns:: The underlying likelihood data structure.

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

virtual double bpp::TreeLikelihood::getLikelihoodForASite ( size_t site ) const [pure virtual, inherited]

Get the likelihood for a site.

Parameters:

site	The site index to analyse.

Returns:: The likelihood for site site.

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

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

virtual double bpp::DiscreteRatesAcrossSitesTreeLikelihood::getLikelihoodForASiteForARateClass	(	size_t	site,
		size_t	rateClass
	)		const `[pure 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.

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

virtual double bpp::DiscreteRatesAcrossSitesTreeLikelihood::getLikelihoodForASiteForARateClassForAState	(	size_t	site,
		size_t	rateClass,
		int	state
	)		const `[pure 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.

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

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().

virtual double bpp::TreeLikelihood::getLogLikelihood ( ) const [pure virtual, inherited]

Get the logarithm of the likelihood for the whole dataset.

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

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

virtual double bpp::TreeLikelihood::getLogLikelihoodForASite ( size_t site ) const [pure 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.

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

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

virtual double bpp::DiscreteRatesAcrossSitesTreeLikelihood::getLogLikelihoodForASiteForARateClass	(	size_t	site,
		size_t	rateClass
	)		const `[pure 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.

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

virtual double bpp::DiscreteRatesAcrossSitesTreeLikelihood::getLogLikelihoodForASiteForARateClassForAState	(	size_t	site,
		size_t	rateClass,
		int	state
	)		const `[pure 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..

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

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]

Definition at line 271 of file AbstractNonHomogeneousTreeLikelihood.h.

References maximumBrLen_.

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

Definition at line 270 of file AbstractNonHomogeneousTreeLikelihood.h.

References minimumBrLen_.

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

Implements bpp::TreeLikelihood.

Definition at line 202 of file AbstractNonHomogeneousTreeLikelihood.h.

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

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

Implements bpp::TreeLikelihood.

Definition at line 207 of file AbstractNonHomogeneousTreeLikelihood.h.

References 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.

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]

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]

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 rootFreqs_.

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

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 modelSet_.

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

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

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]

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 modelSet_.

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

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 modelSet_.

ParameterList AbstractNonHomogeneousTreeLikelihood::getSubstitutionModelParameters ( ) const [virtual]

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 modelSet_.

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

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

Implements bpp::NonHomogeneousTreeLikelihood.

Definition at line 221 of file AbstractNonHomogeneousTreeLikelihood.h.

References modelSet_.

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

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

Implements bpp::NonHomogeneousTreeLikelihood.

Definition at line 223 of file AbstractNonHomogeneousTreeLikelihood.h.

References 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]`

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 pxy_.

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

Get the tree (topology and branch lengths).

Returns:: The tree of this TreeLikelihood object.

Implements bpp::TreeLikelihood.

Definition at line 292 of file AbstractTreeLikelihood.h.

References bpp::AbstractTreeLikelihood::tree_.

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

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

Get the tree (topology and branch lengths).

Returns:: The tree of this TreeLikelihood object.

Implemented in bpp::AbstractTreeLikelihood.

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

void AbstractNonHomogeneousTreeLikelihood::init_	(	const Tree &	tree,
		SubstitutionModelSet *	modelSet,
		DiscreteDistribution *	rDist,
		bool	verbose
	)		throw (Exception) `[private]`

Method called by constructor.

Definition at line 164 of file AbstractNonHomogeneousTreeLikelihood.cpp.

References bpp::TreeTools::checkIds(), bpp::Node::getId(), bpp::TreeTemplate< N >::getRootNode(), and bpp::Node::getSon().

void AbstractNonHomogeneousTreeLikelihood::initBranchLengthsParameters ( ) [virtual]

void AbstractNonHomogeneousTreeLikelihood::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::AbstractTreeLikelihood.

Reimplemented in bpp::RNonHomogeneousMixedTreeLikelihood.

Definition at line 268 of file AbstractNonHomogeneousTreeLikelihood.cpp.

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

void AbstractNonHomogeneousTreeLikelihood::initParameters ( ) [virtual]

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

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

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

Assignation operator.

This operator is to be called by the derived class operator.

Definition at line 128 of file AbstractNonHomogeneousTreeLikelihood.cpp.

References brLenConstraint_, brLenParameters_, d2pxy_, dpxy_, bpp::Node::getId(), bpp::TreeTemplate< N >::getNodes(), idToNode_, maximumBrLen_, minimumBrLen_, modelSet_, nbClasses_, nbDistinctSites_, nbNodes_, nbSites_, nbStates_, nodes_, pxy_, reparametrizeRoot_, root1_, root2_, rootFreqs_, bpp::AbstractTreeLikelihood::tree_, and verbose_.

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().

virtual void bpp::TreeLikelihood::setData ( const SiteContainer & sites ) [pure virtual, inherited]

Set the dataset for which the likelihood must be evaluated.

Parameters:

sites The data set to use.

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

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

Definition at line 260 of file AbstractNonHomogeneousTreeLikelihood.h.

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

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

Definition at line 250 of file AbstractNonHomogeneousTreeLikelihood.h.

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

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

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().

Member Data Documentation

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

Definition at line 127 of file AbstractNonHomogeneousTreeLikelihood.h.

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

ParameterList bpp::AbstractNonHomogeneousTreeLikelihood::brLenParameters_ [protected]

Definition at line 93 of file AbstractNonHomogeneousTreeLikelihood.h.

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

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

Definition at line 227 of file AbstractTreeLikelihood.h.

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

Definition at line 99 of file AbstractNonHomogeneousTreeLikelihood.h.

Referenced by computeTransitionProbabilitiesForNode(), bpp::RNonHomogeneousMixedTreeLikelihood::computeTransitionProbabilitiesForNode(), bpp::RNonHomogeneousTreeLikelihood::computeTreeD2Likelihood(), bpp::DRNonHomogeneousTreeLikelihood::computeTreeD2LikelihoodAtNode(), and 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(), initialize(), bpp::AbstractTreeLikelihood::operator=(), and bpp::AbstractTreeLikelihood::~AbstractTreeLikelihood().

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

Definition at line 97 of file AbstractNonHomogeneousTreeLikelihood.h.

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

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

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

Definition at line 114 of file AbstractNonHomogeneousTreeLikelihood.h.

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

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

Definition at line 229 of file AbstractTreeLikelihood.h.

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

double bpp::AbstractNonHomogeneousTreeLikelihood::maximumBrLen_ [protected]

Definition at line 126 of file AbstractNonHomogeneousTreeLikelihood.h.

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

double bpp::AbstractNonHomogeneousTreeLikelihood::minimumBrLen_ [protected]

Definition at line 125 of file AbstractNonHomogeneousTreeLikelihood.h.

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

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

Definition at line 92 of file AbstractNonHomogeneousTreeLikelihood.h.

Referenced by applyParameters(), computeAllTransitionProbabilities(), computeTransitionProbabilitiesForNode(), bpp::RNonHomogeneousMixedTreeLikelihood::computeTransitionProbabilitiesForNode(), bpp::DRNonHomogeneousTreeLikelihood::fireParameterChanged(), bpp::RNonHomogeneousTreeLikelihood::fireParameterChanged(), bpp::RNonHomogeneousMixedTreeLikelihood::fireParameterChanged(), getNewBranchModelIterator(), getNewSiteModelIterator(), getRootFrequenciesParameters(), getSubstitutionModelForNode(), getSubstitutionModelParameters(), getSubstitutionModelSet(), bpp::RNonHomogeneousMixedTreeLikelihood::init(), initParameters(), and operator=().

size_t bpp::AbstractNonHomogeneousTreeLikelihood::nbClasses_ [protected]

Definition at line 117 of file AbstractNonHomogeneousTreeLikelihood.h.

size_t bpp::AbstractNonHomogeneousTreeLikelihood::nbDistinctSites_ [protected]

Definition at line 117 of file AbstractNonHomogeneousTreeLikelihood.h.

size_t bpp::AbstractNonHomogeneousTreeLikelihood::nbNodes_ [protected]

Definition at line 117 of file AbstractNonHomogeneousTreeLikelihood.h.

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

size_t bpp::AbstractNonHomogeneousTreeLikelihood::nbSites_ [protected]

Definition at line 117 of file AbstractNonHomogeneousTreeLikelihood.h.

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

size_t bpp::AbstractNonHomogeneousTreeLikelihood::nbStates_ [protected]

Definition at line 117 of file AbstractNonHomogeneousTreeLikelihood.h.

std::vector<Node*> bpp::AbstractNonHomogeneousTreeLikelihood::nodes_ [protected]

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.

Referenced by AbstractNonHomogeneousTreeLikelihood(), applyParameters(), computeAllTransitionProbabilities(), bpp::RNonHomogeneousTreeLikelihood::computeTreeD2Likelihood(), bpp::RNonHomogeneousMixedTreeLikelihood::computeTreeD2Likelihood(), bpp::DRNonHomogeneousTreeLikelihood::computeTreeD2Likelihoods(), bpp::RNonHomogeneousTreeLikelihood::computeTreeDLikelihood(), bpp::RNonHomogeneousMixedTreeLikelihood::computeTreeDLikelihood(), bpp::DRNonHomogeneousTreeLikelihood::computeTreeDLikelihoods(), bpp::DRNonHomogeneousTreeLikelihood::fireParameterChanged(), bpp::RNonHomogeneousTreeLikelihood::fireParameterChanged(), bpp::RNonHomogeneousMixedTreeLikelihood::fireParameterChanged(), initBranchLengthsParameters(), and operator=().