bpp::NNIHomogeneousTreeLikelihood Class Reference

This class adds support for NNI topology estimation to the DRHomogeneousTreeLikelihood class. More...

#include <Bpp/Phyl/Legacy/Likelihood/NNIHomogeneousTreeLikelihood.h>

Inheritance diagram for bpp::NNIHomogeneousTreeLikelihood:

Collaboration diagram for bpp::NNIHomogeneousTreeLikelihood:

Public Member Functions
	NNIHomogeneousTreeLikelihood (const Tree &tree, std::shared_ptr< TransitionModelInterface > model, std::shared_ptr< DiscreteDistributionInterface > rDist, bool checkRooted=true, bool verbose=true)
	Build a new NNIHomogeneousTreeLikelihood object. More...
	NNIHomogeneousTreeLikelihood (const Tree &tree, const AlignmentDataInterface &data, std::shared_ptr< TransitionModelInterface > model, std::shared_ptr< DiscreteDistributionInterface > rDist, bool checkRooted=true, bool verbose=true)
	Build a new NNIHomogeneousTreeLikelihood object. More...
	NNIHomogeneousTreeLikelihood (const NNIHomogeneousTreeLikelihood &lik)
	Copy constructor. More...
NNIHomogeneousTreeLikelihood &	operator= (const NNIHomogeneousTreeLikelihood &lik)
virtual	~NNIHomogeneousTreeLikelihood ()
NNIHomogeneousTreeLikelihood *	clone () const override
void	setData (const AlignmentDataInterface &sites) override
	Set the dataset for which the likelihood must be evaluated. More...
void	computeTreeLikelihood ()
void	setParameters (const ParameterList &parameters) override
	Implements the Function interface. More...
double	getValue () const override
	Function and NNISearchable interface. More...
DRASDRTreeLikelihoodData &	likelihoodData () override
const DRASDRTreeLikelihoodData &	likelihoodData () const override
virtual void	computeLikelihoodAtNode (int nodeId, VVVdouble &likelihoodArray) const override
	Compute the likelihood array at a given node. More...
virtual std::shared_ptr< const SubstitutionModelInterface >	getSubstitutionModel () const
	Get a SubstitutionModel pointer toward the model associated to this instance, if possible. More...
virtual std::shared_ptr< const SubstitutionModelInterface >	getSubstitutionModel (int nodeId, size_t siteIndex) const
	Get a SubstitutionModel pointer toward the model associated to this instance, if possible. More...
virtual void	initParameters ()
	This builds the parameters list from all parametrizable objects, i.e. substitution model, rate distribution and tree. More...
virtual void	applyParameters ()
	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. More...
virtual void	initBranchLengthsParameters (bool verbose=true)
virtual void	setMinimumBranchLength (double minimum)
virtual void	setMaximumBranchLength (double maximum)
virtual double	getMinimumBranchLength () const
virtual double	getMaximumBranchLength () const
std::shared_ptr< const TransitionModelInterface >	getModelForSite (int nodeId, size_t siteIndex) const
	Get the substitution model associated to a given node and alignment column. More...
std::shared_ptr< TransitionModelInterface >	getModelForSite (int nodeId, size_t siteIndex)
	Get the substitution model associated to a given node and alignment column. More...
virtual const AlignmentDataInterface &	data () const =0
	Get the dataset for which the likelihood must be evaluated. More...
virtual bool	isInitialized () const =0
virtual bool	hasLikelihoodData () const =0
virtual double	getLikelihoodForASiteForAState (size_t site, int state) const =0
	Get the likelihood for a site and for a state. More...
virtual double	getLogLikelihoodForASiteForAState (size_t site, int state) const =0
	Get the logarithm of the likelihood for a site and for a state. More...
virtual Vdouble	getLikelihoodPerSite () const =0
	Get the likelihood for each site. More...
virtual Vdouble	getLogLikelihoodPerSite () const =0
	Get the logarithm of the likelihood for each site. More...
virtual VVdouble	getLikelihoodPerSitePerState () const =0
	Get the likelihood for each site and for each state. More...
virtual VVdouble	getLogLikelihoodPerSitePerState () const =0
	Get the logarithm of the likelihood for each site and for each state. More...
virtual const Tree &	tree () const =0
	Get the tree (topology and branch lengths). More...
virtual size_t	getNumberOfSites () const =0
	Get the number of sites in the dataset. More...
virtual std::shared_ptr< const Alphabet >	getAlphabet () const =0
	Get the alphabet associated to the dataset. More...
virtual void	enableDerivatives (bool yn)=0
	Tell if derivatives must be computed. More...
virtual ParameterList	getDerivableParameters () const =0
	All derivable parameters. More...
virtual ParameterList	getNonDerivableParameters () const =0
	All non derivable parameters. More...
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 override
virtual const ParameterList &	getParameters () const=0
const ParameterList &	getParameters () const override
virtual const Parameter &	parameter (const std::string &name) const=0
const Parameter &	parameter (const std::string &name) const override
virtual double	getParameterValue (const std::string &name) const=0
double	getParameterValue (const std::string &name) const override
virtual void	setAllParametersValues (const ParameterList &parameters)=0
void	setAllParametersValues (const ParameterList &parameters) override
virtual void	setParameterValue (const std::string &name, double value)=0
void	setParameterValue (const std::string &name, double value) override
virtual void	setParametersValues (const ParameterList &parameters)=0
void	setParametersValues (const ParameterList &parameters) override
virtual bool	matchParametersValues (const ParameterList &parameters)=0
bool	matchParametersValues (const ParameterList &parameters) override
virtual void	removeConstraint (const std::string &name)=0
void	removeConstraint (const std::string &name) override
virtual void	setConstraint (const std::string &name, std::shared_ptr< ConstraintInterface > constraint)=0
void	setConstraint (const std::string &name, std::shared_ptr< ConstraintInterface > constraint) override
virtual size_t	getNumberOfParameters () const=0
size_t	getNumberOfParameters () const override
virtual void	setNamespace (const std::string &prefix)=0
void	setNamespace (const std::string &prefix) override
virtual std::string	getNamespace () const=0
std::string	getNamespace () const override
virtual std::string	getParameterNameWithoutNamespace (const std::string &name) const=0
std::string	getParameterNameWithoutNamespace (const std::string &name) const override
const std::shared_ptr< Parameter > &	getParameter (const std::string &name) const
virtual void	topologyChangePerformed (const TopologyChangeEvent &event)
	Notify a topology change event. More...
The NNISearchable interface.
Current implementation: When testing a particular NNI, only the branch length of the parent node is optimized (and roughly). All other parameters (substitution model, rate distribution and other branch length are kept at there current value. When performing a NNI, only the topology change is performed. This is up to the user to re-initialize the underlying likelihood data to match the new topology. Usually, this is achieved by calling the topologyChangePerformed() method, which call the reInit() method of the LikelihoodData object.
const Tree &	topology () const override
	Get the tree associated to this NNISearchable object. More...
double	getTopologyValue () const override
	Get the current score of this NNISearchable object. More...
double	testNNI (int nodeId) const override
	Send the score of a NNI movement, without performing it. More...
void	doNNI (int nodeId) override
	Perform a NNI movement. More...
void	topologyChangeTested (const TopologyChangeEvent &event) override
	Notify a topology change event. More...
void	topologyChangeSuccessful (const TopologyChangeEvent &event) override
	Tell that a topology change is definitive. More...
The TreeLikelihood interface.
Other methods are implemented in the AbstractTreeLikelihood class.
double	getLikelihood () const override
	Get the likelihood for the whole dataset. More...
double	getLogLikelihood () const override
	Get the logarithm of the likelihood for the whole dataset. More...
double	getLikelihoodForASite (size_t site) const override
	Get the likelihood for a site. More...
double	getLogLikelihoodForASite (size_t site) const override
	Get the logarithm of the likelihood for a site. More...
size_t	getSiteIndex (size_t site) const override
	Get the index (used for inner computations) of a given site (original alignment column). More...
The DiscreteRatesAcrossSites interface implementation:
double	getLikelihoodForASiteForARateClass (size_t site, size_t rateClass) const override
	Get the likelihood for a site knowing its rate class. More...
double	getLogLikelihoodForASiteForARateClass (size_t site, size_t rateClass) const override
	Get the logarithm of the likelihood for a site knowing its rate class. More...
double	getLikelihoodForASiteForARateClassForAState (size_t site, size_t rateClass, int state) const override
	Get the likelihood for a site knowing its rate class and its ancestral state. More...
double	getLogLikelihoodForASiteForARateClassForAState (size_t site, size_t rateClass, int state) const override
	Get the logarithm of the likelihood for a site knowing its rate class and its ancestral state. More...
DerivableFirstOrder interface.
double	getFirstOrderDerivative (const std::string &variable) const override
DerivableSecondOrder interface.
double	getSecondOrderDerivative (const std::string &variable) const override
double	getSecondOrderDerivative (const std::string &variable1, const std::string &variable2) const override
The TreeLikelihood interface.
Other methods are implemented in the AbstractTreeLikelihood class.
size_t	getNumberOfStates () const
const std::vector< int > &	getAlphabetStates () const
int	getAlphabetStateAsInt (size_t i) const
std::string	getAlphabetStateAsChar (size_t i) const
void	initialize ()
	Init the likelihood object. More...
ParameterList	getBranchLengthsParameters () const
	Get the branch lengths parameters. More...
ParameterList	getSubstitutionModelParameters () const
	Get the parameters associated to substitution model(s). More...
ParameterList	getRateDistributionParameters () const
	Get the parameters associated to the rate distribution. More...
const std::vector< double > &	getRootFrequencies (size_t siteIndex) const
	Get the values of the frequencies for each state in the alphabet at the root node. More...
VVVdouble	getTransitionProbabilitiesPerRateClass (int nodeId, size_t siteIndex) const
	Retrieves all Pij(t) for a particular branch, defined by the upper node. More...
ConstBranchModelIterator *	getNewBranchModelIterator (int nodeId) const
ConstSiteModelIterator *	getNewSiteModelIterator (size_t siteIndex) const
The HomogeneousTreeLikelihood interface.
Other methods are implemented in the AbstractTreeLikelihood class.
std::shared_ptr< const TransitionModelInterface >	getModel () const
std::shared_ptr< const TransitionModelInterface >	getModel (int nodeId, size_t siteIndex) const
std::shared_ptr< TransitionModelInterface >	getModel ()
std::shared_ptr< TransitionModelInterface >	getModel (int nodeId, size_t siteIndex)
void	setModel (std::shared_ptr< TransitionModelInterface > model)
The TreeLikelihood interface.
const AlignmentDataInterface &	data () const
	Get the dataset for which the likelihood must be evaluated. More...
bool	isInitialized () const
bool	hasLikelihoodData () const
Vdouble	getLikelihoodPerSite () const
	Get the likelihood for each site. More...
Vdouble	getLogLikelihoodPerSite () const
	Get the logarithm of the likelihood for each site. More...
VVdouble	getLikelihoodPerSitePerState () const
	Get the likelihood for each site and for each state. More...
VVdouble	getLogLikelihoodPerSitePerState () const
	Get the logarithm of the likelihood for each site and for each state. More...
const Tree &	tree () const
	Get the tree (topology and branch lengths). More...
size_t	getNumberOfSites () const
	Get the number of sites in the dataset. More...
std::shared_ptr< const Alphabet >	getAlphabet () const
	Get the alphabet associated to the dataset. More...
void	enableDerivatives (bool yn)
	Tell if derivatives must be computed. More...
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. More...
double	getLogLikelihoodForASiteForAState (size_t site, int state) const
	Get the logarithm of the likelihood for a site and for a state. More...
VVdouble	getTransitionProbabilities (int nodeId, size_t siteIndex) const
	Retrieves all Pij(t) for a particular branch, defined by the upper node and site. More...
ParameterList	getDerivableParameters () const
	All derivable parameters. More...
ParameterList	getNonDerivableParameters () const
	All non derivable parameters. More...
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. More...
The DiscreteRatesAcrossSites interface implementation:
std::shared_ptr< const DiscreteDistributionInterface >	getRateDistribution () const
	Get the rate distribution used for the computation. More...
std::shared_ptr< DiscreteDistributionInterface >	getRateDistribution ()
	Get the rate distribution used for the computation. More...
const DiscreteDistributionInterface &	rateDistribution () const
	Get the rate distribution used for the computation. More...
DiscreteDistributionInterface &	rateDistribution ()
	Get the rate distribution used for the computation. More...
size_t	getNumberOfClasses () const
	Get the number of classes. More...
VVdouble	getLikelihoodPerSitePerRateClass () const
	Get the likelihood for each site and each rate class. More...
VVdouble	getLogLikelihoodPerSitePerRateClass () const
	Get the logarithm of the likelihood for each site and each rate class. More...
VVVdouble	getLikelihoodPerSitePerRateClassPerState () const
	Get the likelihood for each site and each rate class and each state. More...
VVVdouble	getLogLikelihoodPerSitePerRateClassPerState () const
	Get the logarithm of the likelihood for each site and each rate class and each state. More...
VVdouble	getPosteriorProbabilitiesPerRate () const
	Get the posterior probability for each site of belonging to a particular rate class. More...
Vdouble	getRateWithMaxPostProbPerSite () const
	Get the posterior rate (the one with maximum posterior probability) for each site. More...
std::vector< size_t >	getRateClassWithMaxPostProbPerSite () const
	Get the posterior rate class (the one with maximum posterior probability) for each site. More...
Vdouble	getPosteriorRatePerSite () const
	Get the posterior rate, i.e. averaged over all classes and weighted with posterior probabilities, for each site. More...

Static Public Member Functions
Generic tools to deal with likelihood arrays
static void	resetLikelihoodArray (VVVdouble &likelihoodArray)
	Set all conditional likelihoods to 1. More...
static void	displayLikelihoodArray (const VVVdouble &likelihoodArray)
	Print the likelihood array to terminal (debugging tool). More...

Protected Member Functions
virtual void	computeLikelihoodAtNode_ (const Node *node, VVVdouble &likelihoodArray, const Node *sonNode=0) const
virtual void	computeSubtreeLikelihoodPostfix (const Node *node)
virtual void	computeSubtreeLikelihoodPrefix (const Node *node)
virtual void	computeRootLikelihood ()
virtual void	computeTreeDLikelihoodAtNode (const Node *node)
virtual void	computeTreeDLikelihoods ()
virtual void	computeTreeD2LikelihoodAtNode (const Node *node)
virtual void	computeTreeD2Likelihoods ()
virtual void	fireParameterChanged (const ParameterList &params) override
virtual void	resetLikelihoodArrays (const Node *node)
virtual void	displayLikelihood (const Node *node)
	This method is mainly for debugging purpose. More...
virtual void	computeAllTransitionProbabilities ()
	Fill the pxy_, dpxy_ and d2pxy_ arrays for all nodes. More...
virtual void	computeTransitionProbabilitiesForNode (const Node *node)
	Fill the pxy_, dpxy_ and d2pxy_ arrays for one node. More...
virtual ParameterList &	getParameters_ ()=0
ParameterList &	getParameters_ () override
const std::shared_ptr< Parameter > &	getParameter (size_t i) const
std::shared_ptr< Parameter > &	getParameter (size_t i)
virtual void	addParameter_ (Parameter *parameter)
virtual void	addParameters_ (const ParameterList &parameters)
virtual void	shareParameter_ (const std::shared_ptr< Parameter > &parameter)
virtual void	shareParameters_ (const ParameterList &parameters)
virtual void	includeParameters_ (const ParameterList &parameters)
virtual void	deleteParameter_ (size_t index)
virtual void	deleteParameter_ (std::string &name)
virtual void	deleteParameters_ (const std::vector< std::string > &names)
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

Static Protected Member Functions
static void	computeLikelihoodFromArrays (const std::vector< const VVVdouble * > &iLik, const std::vector< const VVVdouble * > &tProb, VVVdouble &oLik, size_t nbNodes, size_t nbDistinctSites, size_t nbClasses, size_t nbStates, bool reset=true)
	Compute conditional likelihoods. More...
static void	computeLikelihoodFromArrays (const std::vector< const VVVdouble * > &iLik, const std::vector< const VVVdouble * > &tProb, const VVVdouble *iLikR, const VVVdouble *tProbR, VVVdouble &oLik, size_t nbNodes, size_t nbDistinctSites, size_t nbClasses, size_t nbStates, bool reset=true)
	Compute conditional likelihoods. More...

Protected Attributes
std::shared_ptr< BranchLikelihood >	brLikFunction_
std::unique_ptr< BrentOneDimension >	brentOptimizer_
	Optimizer used for testing NNI. More...
std::map< int, double >	brLenNNIValues_
	Hash used for backing up branch lengths when testing NNIs. More...
ParameterList	brLenNNIParams_
double	minusLogLik_
std::shared_ptr< TransitionModelInterface >	model_
ParameterList	brLenParameters_
std::map< int, VVVdouble >	pxy_
std::map< int, VVVdouble >	dpxy_
std::map< int, VVVdouble >	d2pxy_
std::vector< double >	rootFreqs_
std::vector< Node * >	nodes_
	Pointer toward all nodes in the tree. More...
size_t	nbSites_
size_t	nbDistinctSites_
size_t	nbClasses_
size_t	nbStates_
size_t	nbNodes_
bool	verbose_
double	minimumBrLen_
double	maximumBrLen_
std::shared_ptr< ConstraintInterface >	brLenConstraint_
std::shared_ptr< DiscreteDistributionInterface >	rateDistribution_
std::unique_ptr< const AlignmentDataInterface >	data_
std::shared_ptr< TreeTemplate< Node > >	tree_
bool	computeFirstOrderDerivatives_
bool	computeSecondOrderDerivatives_
bool	initialized_

Private Member Functions
void	init_ ()
	Method called by constructors. More...

Private Attributes
std::unique_ptr< DRASDRTreeLikelihoodData >	likelihoodData_
ParameterList	parameters_
std::string	prefix_

Detailed Description

This class adds support for NNI topology estimation to the DRHomogeneousTreeLikelihood class.

Definition at line 131 of file NNIHomogeneousTreeLikelihood.h.

Constructor & Destructor Documentation

NNIHomogeneousTreeLikelihood() [1/3]

NNIHomogeneousTreeLikelihood::NNIHomogeneousTreeLikelihood	(	const Tree &	tree,
		std::shared_ptr< TransitionModelInterface >	model,
		std::shared_ptr< DiscreteDistributionInterface >	rDist,
		bool	checkRooted = true,
		bool	verbose = true
	)

Build a new NNIHomogeneousTreeLikelihood object.

Parameters

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

Exceptions

Exception

in an error occurred.

Definition at line 91 of file NNIHomogeneousTreeLikelihood.cpp.

References brentOptimizer_, and bpp::AutoParameter::CONSTRAINTS_AUTO.

Referenced by clone().

NNIHomogeneousTreeLikelihood() [2/3]

NNIHomogeneousTreeLikelihood::NNIHomogeneousTreeLikelihood	(	const Tree &	tree,
		const AlignmentDataInterface &	data,
		std::shared_ptr< TransitionModelInterface >	model,
		std::shared_ptr< DiscreteDistributionInterface >	rDist,
		bool	checkRooted = true,
		bool	verbose = true
	)

Build a new NNIHomogeneousTreeLikelihood object.

Parameters

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

Exceptions

Exception

in an error occurred.

Definition at line 112 of file NNIHomogeneousTreeLikelihood.cpp.

References brentOptimizer_, brLikFunction_, bpp::AutoParameter::CONSTRAINTS_AUTO, and bpp::DRHomogeneousTreeLikelihood::likelihoodData().

NNIHomogeneousTreeLikelihood() [3/3]

NNIHomogeneousTreeLikelihood::NNIHomogeneousTreeLikelihood

(

const NNIHomogeneousTreeLikelihood &

lik

)

Copy constructor.

Definition at line 136 of file NNIHomogeneousTreeLikelihood.cpp.

References brentOptimizer_, brLenNNIParams_, brLenNNIValues_, and brLikFunction_.

~NNIHomogeneousTreeLikelihood()

NNIHomogeneousTreeLikelihood::~NNIHomogeneousTreeLikelihood ( )

virtual

Definition at line 163 of file NNIHomogeneousTreeLikelihood.cpp.

Member Function Documentation

applyParameters()

void AbstractHomogeneousTreeLikelihood::applyParameters ( )

virtualinherited

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 249 of file AbstractHomogeneousTreeLikelihood.cpp.

References bpp::AbstractParametrizable::getParameters(), bpp::Parameter::getValue(), bpp::AbstractTreeLikelihood::initialized_, bpp::AbstractHomogeneousTreeLikelihood::model_, bpp::AbstractHomogeneousTreeLikelihood::nbNodes_, bpp::AbstractHomogeneousTreeLikelihood::nodes_, bpp::AbstractParametrizable::parameter(), bpp::AbstractDiscreteRatesAcrossSitesTreeLikelihood::rateDistribution_, bpp::AbstractHomogeneousTreeLikelihood::rootFreqs_, and bpp::TextTools::toString().

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

clone()

NNIHomogeneousTreeLikelihood* bpp::NNIHomogeneousTreeLikelihood::clone ( ) const

inlineoverridevirtual

Reimplemented from bpp::DRHomogeneousTreeLikelihood.

Definition at line 198 of file NNIHomogeneousTreeLikelihood.h.

References NNIHomogeneousTreeLikelihood().

computeAllTransitionProbabilities()

void AbstractHomogeneousTreeLikelihood::computeAllTransitionProbabilities ( )

protectedvirtualinherited

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

Reimplemented in bpp::RHomogeneousMixedTreeLikelihood.

Definition at line 306 of file AbstractHomogeneousTreeLikelihood.cpp.

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

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

computeLikelihoodAtNode()

virtual void bpp::DRHomogeneousTreeLikelihood::computeLikelihoodAtNode ( int  nodeId, VVVdouble &  likelihoodArray  ) const

inlineoverridevirtualinherited

Compute the likelihood array at a given node.

Parameters

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

Implements bpp::DRTreeLikelihoodInterface.

Definition at line 170 of file DRHomogeneousTreeLikelihood.h.

References bpp::DRHomogeneousTreeLikelihood::computeLikelihoodAtNode_(), and bpp::AbstractTreeLikelihood::tree_.

computeLikelihoodAtNode_()

void DRHomogeneousTreeLikelihood::computeLikelihoodAtNode_ ( const Node *  node, VVVdouble &  likelihoodArray, const Node *  sonNode = 0  ) const

protectedvirtualinherited

Reimplemented in bpp::DRHomogeneousMixedTreeLikelihood.

Definition at line 682 of file DRHomogeneousTreeLikelihood.cpp.

References bpp::DRHomogeneousTreeLikelihood::computeLikelihoodFromArrays(), bpp::Node::getFather(), bpp::Node::getId(), bpp::Node::getNumberOfSons(), bpp::Node::getSon(), bpp::Node::hasFather(), bpp::Node::isLeaf(), bpp::DRHomogeneousTreeLikelihood::likelihoodData_, bpp::AbstractHomogeneousTreeLikelihood::nbClasses_, bpp::AbstractHomogeneousTreeLikelihood::nbDistinctSites_, bpp::AbstractHomogeneousTreeLikelihood::nbStates_, bpp::AbstractHomogeneousTreeLikelihood::pxy_, and bpp::AbstractHomogeneousTreeLikelihood::rootFreqs_.

Referenced by bpp::DRHomogeneousTreeLikelihood::computeLikelihoodAtNode(), bpp::DRHomogeneousTreeLikelihood::computeTreeD2LikelihoodAtNode(), and bpp::DRHomogeneousTreeLikelihood::computeTreeDLikelihoodAtNode().

computeLikelihoodFromArrays() [1/2]

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

staticprotectedinherited

Compute conditional likelihoods.

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

Parameters

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

Definition at line 831 of file DRHomogeneousTreeLikelihood.cpp.

References bpp::AbstractDiscreteRatesAcrossSitesTreeLikelihood::resetLikelihoodArray().

computeLikelihoodFromArrays() [2/2]

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

staticprotectedinherited

Compute conditional likelihoods.

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

Parameters

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

Definition at line 782 of file DRHomogeneousTreeLikelihood.cpp.

References bpp::AbstractDiscreteRatesAcrossSitesTreeLikelihood::resetLikelihoodArray().

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

computeRootLikelihood()

void DRHomogeneousTreeLikelihood::computeRootLikelihood ( )

protectedvirtualinherited

Reimplemented in bpp::DRHomogeneousMixedTreeLikelihood.

Definition at line 612 of file DRHomogeneousTreeLikelihood.cpp.

References bpp::DRHomogeneousTreeLikelihood::computeLikelihoodFromArrays(), bpp::Node::getId(), bpp::Node::getNumberOfSons(), bpp::Node::getSon(), bpp::Node::isLeaf(), bpp::DRHomogeneousTreeLikelihood::likelihoodData_, bpp::AbstractHomogeneousTreeLikelihood::nbClasses_, bpp::AbstractHomogeneousTreeLikelihood::nbDistinctSites_, bpp::AbstractHomogeneousTreeLikelihood::nbStates_, bpp::AbstractHomogeneousTreeLikelihood::pxy_, bpp::AbstractDiscreteRatesAcrossSitesTreeLikelihood::rateDistribution_, bpp::AbstractDiscreteRatesAcrossSitesTreeLikelihood::resetLikelihoodArray(), bpp::AbstractHomogeneousTreeLikelihood::rootFreqs_, and bpp::AbstractTreeLikelihood::tree_.

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

computeSubtreeLikelihoodPostfix()

void DRHomogeneousTreeLikelihood::computeSubtreeLikelihoodPostfix ( const Node *  node )

protectedvirtualinherited

Initialize the arrays corresponding to each son node for the node passed as argument. The method is called for each son node and the result stored in the corresponding array.

Reimplemented in bpp::DRHomogeneousMixedTreeLikelihood.

Definition at line 442 of file DRHomogeneousTreeLikelihood.cpp.

References bpp::DRHomogeneousTreeLikelihood::computeLikelihoodFromArrays(), bpp::Node::getId(), bpp::Node::getNumberOfSons(), bpp::Node::getSon(), bpp::Node::isLeaf(), bpp::DRHomogeneousTreeLikelihood::likelihoodData_, bpp::AbstractHomogeneousTreeLikelihood::nbClasses_, bpp::AbstractHomogeneousTreeLikelihood::nbDistinctSites_, bpp::AbstractHomogeneousTreeLikelihood::nbStates_, bpp::AbstractHomogeneousTreeLikelihood::pxy_, and bpp::DRHomogeneousTreeLikelihood::resetLikelihoodArrays().

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

computeSubtreeLikelihoodPrefix()

void DRHomogeneousTreeLikelihood::computeSubtreeLikelihoodPrefix ( const Node *  node )

protectedvirtualinherited

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

Reimplemented in bpp::DRHomogeneousMixedTreeLikelihood.

Definition at line 502 of file DRHomogeneousTreeLikelihood.cpp.

References bpp::DRHomogeneousTreeLikelihood::computeLikelihoodFromArrays(), bpp::Node::getFather(), bpp::Node::getId(), bpp::Node::getNumberOfSons(), bpp::Node::getSon(), bpp::Node::hasFather(), bpp::Node::isLeaf(), bpp::DRHomogeneousTreeLikelihood::likelihoodData_, bpp::AbstractHomogeneousTreeLikelihood::nbClasses_, bpp::AbstractHomogeneousTreeLikelihood::nbDistinctSites_, bpp::AbstractHomogeneousTreeLikelihood::nbStates_, bpp::AbstractHomogeneousTreeLikelihood::pxy_, bpp::AbstractDiscreteRatesAcrossSitesTreeLikelihood::resetLikelihoodArray(), and bpp::AbstractHomogeneousTreeLikelihood::rootFreqs_.

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

computeTransitionProbabilitiesForNode()

void AbstractHomogeneousTreeLikelihood::computeTransitionProbabilitiesForNode ( const Node *  node )

protectedvirtualinherited

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

Reimplemented in bpp::RHomogeneousMixedTreeLikelihood.

Definition at line 319 of file AbstractHomogeneousTreeLikelihood.cpp.

References bpp::AbstractTreeLikelihood::computeFirstOrderDerivatives_, bpp::AbstractTreeLikelihood::computeSecondOrderDerivatives_, bpp::AbstractHomogeneousTreeLikelihood::d2pxy_, bpp::AbstractHomogeneousTreeLikelihood::dpxy_, bpp::Node::getDistanceToFather(), bpp::Node::getId(), bpp::AbstractHomogeneousTreeLikelihood::model_, bpp::AbstractHomogeneousTreeLikelihood::nbClasses_, bpp::AbstractHomogeneousTreeLikelihood::nbStates_, bpp::AbstractHomogeneousTreeLikelihood::pxy_, and bpp::AbstractDiscreteRatesAcrossSitesTreeLikelihood::rateDistribution_.

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

computeTreeD2LikelihoodAtNode()

void DRHomogeneousTreeLikelihood::computeTreeD2LikelihoodAtNode ( const Node *  node )

protectedvirtualinherited

Reimplemented in bpp::DRHomogeneousMixedTreeLikelihood.

Definition at line 332 of file DRHomogeneousTreeLikelihood.cpp.

References bpp::DRHomogeneousTreeLikelihood::computeLikelihoodAtNode_(), bpp::AbstractHomogeneousTreeLikelihood::d2pxy_, bpp::Node::getFather(), bpp::Node::getId(), bpp::DRHomogeneousTreeLikelihood::likelihoodData_, bpp::AbstractHomogeneousTreeLikelihood::nbClasses_, bpp::AbstractHomogeneousTreeLikelihood::nbDistinctSites_, bpp::AbstractHomogeneousTreeLikelihood::nbStates_, and bpp::AbstractDiscreteRatesAcrossSitesTreeLikelihood::rateDistribution_.

Referenced by bpp::DRHomogeneousTreeLikelihood::computeTreeD2Likelihoods().

computeTreeD2Likelihoods()

void DRHomogeneousTreeLikelihood::computeTreeD2Likelihoods ( )

protectedvirtualinherited

Reimplemented in bpp::DRHomogeneousMixedTreeLikelihood.

Definition at line 374 of file DRHomogeneousTreeLikelihood.cpp.

References bpp::DRHomogeneousTreeLikelihood::computeTreeD2LikelihoodAtNode(), bpp::AbstractHomogeneousTreeLikelihood::nbNodes_, and bpp::AbstractHomogeneousTreeLikelihood::nodes_.

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

computeTreeDLikelihoodAtNode()

void DRHomogeneousTreeLikelihood::computeTreeDLikelihoodAtNode ( const Node *  node )

protectedvirtualinherited

Definition at line 243 of file DRHomogeneousTreeLikelihood.cpp.

References bpp::DRHomogeneousTreeLikelihood::computeLikelihoodAtNode_(), bpp::AbstractHomogeneousTreeLikelihood::dpxy_, bpp::Node::getFather(), bpp::Node::getId(), bpp::DRHomogeneousTreeLikelihood::likelihoodData_, bpp::AbstractHomogeneousTreeLikelihood::nbClasses_, bpp::AbstractHomogeneousTreeLikelihood::nbDistinctSites_, bpp::AbstractHomogeneousTreeLikelihood::nbStates_, and bpp::AbstractDiscreteRatesAcrossSitesTreeLikelihood::rateDistribution_.

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

computeTreeDLikelihoods()

void DRHomogeneousTreeLikelihood::computeTreeDLikelihoods ( )

protectedvirtualinherited

Reimplemented in bpp::DRHomogeneousMixedTreeLikelihood.

Definition at line 288 of file DRHomogeneousTreeLikelihood.cpp.

References bpp::DRHomogeneousTreeLikelihood::computeTreeDLikelihoodAtNode(), bpp::AbstractHomogeneousTreeLikelihood::nbNodes_, and bpp::AbstractHomogeneousTreeLikelihood::nodes_.

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

computeTreeLikelihood()

void DRHomogeneousTreeLikelihood::computeTreeLikelihood ( )

inherited

Definition at line 433 of file DRHomogeneousTreeLikelihood.cpp.

References bpp::DRHomogeneousTreeLikelihood::computeRootLikelihood(), bpp::DRHomogeneousTreeLikelihood::computeSubtreeLikelihoodPostfix(), bpp::DRHomogeneousTreeLikelihood::computeSubtreeLikelihoodPrefix(), and bpp::AbstractTreeLikelihood::tree_.

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

data() [1/2]

const AlignmentDataInterface& bpp::AbstractTreeLikelihood::data ( ) const

inlinevirtualinherited

Get the dataset for which the likelihood must be evaluated.

Returns

The site container where the sequences are stored.

Implements bpp::TreeLikelihoodInterface.

Definition at line 262 of file AbstractTreeLikelihood.h.

References bpp::AbstractTreeLikelihood::data_.

Referenced by bpp::DRHomogeneousMixedTreeLikelihood::DRHomogeneousMixedTreeLikelihood(), bpp::DRHomogeneousTreeLikelihood::DRHomogeneousTreeLikelihood(), bpp::DRNonHomogeneousTreeLikelihood::DRNonHomogeneousTreeLikelihood(), bpp::RNonHomogeneousMixedTreeLikelihood::init(), bpp::RHomogeneousMixedTreeLikelihood::RHomogeneousMixedTreeLikelihood(), bpp::RHomogeneousTreeLikelihood::RHomogeneousTreeLikelihood(), bpp::RNonHomogeneousMixedTreeLikelihood::RNonHomogeneousMixedTreeLikelihood(), and bpp::RNonHomogeneousTreeLikelihood::RNonHomogeneousTreeLikelihood().

data() [2/2]

virtual const AlignmentDataInterface& bpp::TreeLikelihoodInterface::data ( ) const

pure virtualinherited

Get the dataset for which the likelihood must be evaluated.

Returns

The site container where the sequences are stored.

Implemented in bpp::AbstractTreeLikelihood.

displayLikelihood()

void DRHomogeneousTreeLikelihood::displayLikelihood ( const Node *  node )

protectedvirtualinherited

This method is mainly for debugging purpose.

Parameters

node	The node at which likelihood values must be displayed.

Reimplemented in bpp::DRHomogeneousMixedTreeLikelihood.

Definition at line 913 of file DRHomogeneousTreeLikelihood.cpp.

References bpp::AbstractDiscreteRatesAcrossSitesTreeLikelihood::displayLikelihoodArray(), bpp::Node::getFather(), bpp::Node::getId(), bpp::Node::getNumberOfSons(), bpp::Node::getSon(), bpp::Node::hasFather(), and bpp::DRHomogeneousTreeLikelihood::likelihoodData_.

displayLikelihoodArray()

void AbstractDiscreteRatesAcrossSitesTreeLikelihood::displayLikelihoodArray ( const VVVdouble &  likelihoodArray )

staticinherited

Print the likelihood array to terminal (debugging tool).

Parameters

likelihoodArray

the likelihood array.

Definition at line 251 of file AbstractDiscreteRatesAcrossSitesTreeLikelihood.cpp.

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

doNNI()

void NNIHomogeneousTreeLikelihood::doNNI ( int  nodeId )

overridevirtual

Perform a NNI movement.

Parameters

nodeId

The id of the node defining the NNI movement.

Exceptions

NodeException

If the node does not define a valid NNI.

Implements bpp::NNISearchable.

Definition at line 278 of file NNIHomogeneousTreeLikelihood.cpp.

References bpp::ParameterList::addParameter(), bpp::Node::addSon(), brLenNNIParams_, brLenNNIValues_, bpp::AbstractHomogeneousTreeLikelihood::brLenParameters_, bpp::Node::getFather(), bpp::Node::getId(), bpp::AbstractParametrizable::getParameter_(), bpp::Node::getSon(), bpp::Node::getSonPosition(), bpp::Node::hasFather(), bpp::AbstractHomogeneousTreeLikelihood::nodes_, bpp::ParameterList::parameter(), bpp::ParameterList::printParameters(), bpp::Node::removeSon(), bpp::Node::setDistanceToFather(), bpp::ParameterList::setParameterValue(), bpp::Parameter::setValue(), bpp::ParameterList::size(), bpp::TextTools::toString(), and bpp::AbstractTreeLikelihood::tree_.

enableDerivatives() [1/2]

void bpp::AbstractTreeLikelihood::enableDerivatives ( bool  yn )

inlinevirtualinherited

Tell if derivatives must be computed.

This methods calls the enableFirstOrderDerivatives and enableSecondOrderDerivatives.

Parameters

yn	Yes or no.

Implements bpp::TreeLikelihoodInterface.

Definition at line 270 of file AbstractTreeLikelihood.h.

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

Referenced by bpp::AbstractDiscreteRatesAcrossSitesTreeLikelihood::AbstractDiscreteRatesAcrossSitesTreeLikelihood().

enableDerivatives() [2/2]

virtual void bpp::TreeLikelihoodInterface::enableDerivatives ( bool  yn )

pure virtualinherited

Tell if derivatives must be computed.

This methods calls the enableFirstOrderDerivatives and enableSecondOrderDerivatives.

Parameters

yn	Yes or no.

Implemented in bpp::AbstractTreeLikelihood.

enableFirstOrderDerivatives() [1/2]

bool bpp::AbstractTreeLikelihood::enableFirstOrderDerivatives ( ) const

inlinevirtualinherited

Implements bpp::SecondOrderDerivable.

Definition at line 273 of file AbstractTreeLikelihood.h.

References bpp::AbstractTreeLikelihood::computeFirstOrderDerivatives_.

enableFirstOrderDerivatives() [2/2]

void bpp::AbstractTreeLikelihood::enableFirstOrderDerivatives ( bool  yn )

inlinevirtualinherited

Implements bpp::SecondOrderDerivable.

Definition at line 271 of file AbstractTreeLikelihood.h.

References bpp::AbstractTreeLikelihood::computeFirstOrderDerivatives_.

enableSecondOrderDerivatives() [1/2]

bool bpp::AbstractTreeLikelihood::enableSecondOrderDerivatives ( ) const

inlinevirtualinherited

Implements bpp::SecondOrderDerivable.

Definition at line 274 of file AbstractTreeLikelihood.h.

References bpp::AbstractTreeLikelihood::computeSecondOrderDerivatives_.

enableSecondOrderDerivatives() [2/2]

void bpp::AbstractTreeLikelihood::enableSecondOrderDerivatives ( bool  yn )

inlinevirtualinherited

Implements bpp::SecondOrderDerivable.

Definition at line 272 of file AbstractTreeLikelihood.h.

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

fireParameterChanged()

void DRHomogeneousTreeLikelihood::fireParameterChanged ( const ParameterList &  params )

overrideprotectedvirtualinherited

Reimplemented from bpp::AbstractParametrizable.

Reimplemented in bpp::DRHomogeneousMixedTreeLikelihood.

Definition at line 194 of file DRHomogeneousTreeLikelihood.cpp.

References bpp::AbstractHomogeneousTreeLikelihood::applyParameters(), bpp::AbstractHomogeneousTreeLikelihood::computeAllTransitionProbabilities(), bpp::AbstractTreeLikelihood::computeFirstOrderDerivatives_, bpp::AbstractTreeLikelihood::computeSecondOrderDerivatives_, bpp::AbstractHomogeneousTreeLikelihood::computeTransitionProbabilitiesForNode(), bpp::DRHomogeneousTreeLikelihood::computeTreeD2Likelihoods(), bpp::DRHomogeneousTreeLikelihood::computeTreeDLikelihoods(), bpp::DRHomogeneousTreeLikelihood::computeTreeLikelihood(), bpp::DRHomogeneousTreeLikelihood::getLogLikelihood(), bpp::DRHomogeneousTreeLikelihood::minusLogLik_, bpp::AbstractHomogeneousTreeLikelihood::model_, bpp::AbstractHomogeneousTreeLikelihood::nodes_, bpp::AbstractDiscreteRatesAcrossSitesTreeLikelihood::rateDistribution_, and bpp::ParameterList::size().

Referenced by topologyChangeTested().

getAlphabet() [1/2]

std::shared_ptr<const Alphabet> bpp::AbstractTreeLikelihood::getAlphabet ( ) const

inlinevirtualinherited

Get the alphabet associated to the dataset.

Returns

the alphabet associated to the dataset.

Implements bpp::TreeLikelihoodInterface.

Definition at line 263 of file AbstractTreeLikelihood.h.

References bpp::AbstractTreeLikelihood::data_.

getAlphabet() [2/2]

virtual std::shared_ptr<const Alphabet> bpp::TreeLikelihoodInterface::getAlphabet ( ) const

pure virtualinherited

Get the alphabet associated to the dataset.

Returns

the alphabet associated to the dataset.

Implemented in bpp::AbstractTreeLikelihood.

getAlphabetStateAsChar()

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

inlinevirtualinherited

Returns

the alphabet state corresponding to the given model state.

Implements bpp::TreeLikelihoodInterface.

Definition at line 132 of file AbstractHomogeneousTreeLikelihood.h.

References bpp::AbstractHomogeneousTreeLikelihood::model_.

getAlphabetStateAsInt()

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

inlinevirtualinherited

Returns

the alphabet state corresponding to the given model state.

Implements bpp::TreeLikelihoodInterface.

Definition at line 130 of file AbstractHomogeneousTreeLikelihood.h.

References bpp::AbstractHomogeneousTreeLikelihood::model_.

getAlphabetStates()

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

inlinevirtualinherited

Returns

the alphabet states corresponding to all model states.

Implements bpp::TreeLikelihoodInterface.

Definition at line 128 of file AbstractHomogeneousTreeLikelihood.h.

References bpp::AbstractHomogeneousTreeLikelihood::model_.

getBranchLengthsParameters()

ParameterList AbstractHomogeneousTreeLikelihood::getBranchLengthsParameters ( ) const

virtualinherited

Get the branch lengths parameters.

Returns

A ParameterList with all branch lengths.

Implements bpp::TreeLikelihoodInterface.

Definition at line 213 of file AbstractHomogeneousTreeLikelihood.cpp.

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

getDerivableParameters() [1/2]

ParameterList AbstractDiscreteRatesAcrossSitesTreeLikelihood::getDerivableParameters ( ) const

virtualinherited

All derivable parameters.

Usually, this contains all branch lengths parameters.

Returns

A ParameterList.

Implements bpp::TreeLikelihoodInterface.

Definition at line 37 of file AbstractDiscreteRatesAcrossSitesTreeLikelihood.cpp.

References bpp::TreeLikelihoodInterface::getBranchLengthsParameters(), and bpp::AbstractTreeLikelihood::initialized_.

getDerivableParameters() [2/2]

virtual ParameterList bpp::TreeLikelihoodInterface::getDerivableParameters ( ) const

pure virtualinherited

All derivable parameters.

Usually, this contains all branch lengths parameters.

Returns

A ParameterList.

Implemented in bpp::AbstractDiscreteRatesAcrossSitesTreeLikelihood.

getFirstOrderDerivative()

double DRHomogeneousTreeLikelihood::getFirstOrderDerivative ( const std::string &  variable ) const

overridevirtualinherited

Implements bpp::SecondOrderDerivable.

Definition at line 298 of file DRHomogeneousTreeLikelihood.cpp.

References bpp::Node::getId(), bpp::AbstractHomogeneousTreeLikelihood::getRateDistributionParameters(), bpp::AbstractHomogeneousTreeLikelihood::getSubstitutionModelParameters(), bpp::AbstractParametrizable::hasParameter(), bpp::DRHomogeneousTreeLikelihood::likelihoodData_, bpp::AbstractHomogeneousTreeLikelihood::nbDistinctSites_, and bpp::AbstractHomogeneousTreeLikelihood::nodes_.

getLikelihood()

double DRHomogeneousTreeLikelihood::getLikelihood ( ) const

overridevirtualinherited

Get the likelihood for the whole dataset.

Returns

The likelihood of the dataset.

Implements bpp::TreeLikelihoodInterface.

Definition at line 110 of file DRHomogeneousTreeLikelihood.cpp.

References bpp::DRHomogeneousTreeLikelihood::likelihoodData_, bpp::AbstractHomogeneousTreeLikelihood::nbDistinctSites_, and bpp::pow().

getLikelihoodForASite()

double DRHomogeneousTreeLikelihood::getLikelihoodForASite ( size_t  site ) const

overridevirtualinherited

Get the likelihood for a site.

Parameters

site	The site index to analyse.

Returns

The likelihood for site site.

Implements bpp::TreeLikelihoodInterface.

Definition at line 146 of file DRHomogeneousTreeLikelihood.cpp.

References bpp::DRHomogeneousTreeLikelihood::likelihoodData_.

getLikelihoodForASiteForARateClass()

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

overridevirtualinherited

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::DiscreteRatesAcrossSitesTreeLikelihoodInterface.

Definition at line 159 of file DRHomogeneousTreeLikelihood.cpp.

References bpp::DRHomogeneousTreeLikelihood::likelihoodData_.

getLikelihoodForASiteForARateClassForAState()

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

overridevirtualinherited

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::DiscreteRatesAcrossSitesTreeLikelihoodInterface.

Definition at line 173 of file DRHomogeneousTreeLikelihood.cpp.

References bpp::DRHomogeneousTreeLikelihood::likelihoodData_.

getLikelihoodForASiteForAState() [1/2]

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

virtualinherited

Get the likelihood for a site and for a state.

Parameters

site	The site index to analyse.
state	The state to consider.

Returns

The likelihood for site site and state state.

Implements bpp::TreeLikelihoodInterface.

Definition at line 75 of file AbstractDiscreteRatesAcrossSitesTreeLikelihood.cpp.

References bpp::DiscreteRatesAcrossSitesTreeLikelihoodInterface::getLikelihoodForASiteForARateClassForAState(), bpp::AbstractDiscreteRatesAcrossSitesTreeLikelihood::getNumberOfClasses(), and bpp::AbstractDiscreteRatesAcrossSitesTreeLikelihood::rateDistribution_.

getLikelihoodForASiteForAState() [2/2]

virtual double bpp::TreeLikelihoodInterface::getLikelihoodForASiteForAState ( size_t  site, int  state  ) const

pure virtualinherited

Get the likelihood for a site and for a state.

Parameters

site	The site index to analyse.
state	The state to consider.

Returns

The likelihood for site site and state state.

Implemented in bpp::AbstractDiscreteRatesAcrossSitesTreeLikelihood.

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

getLikelihoodPerSite() [1/2]

Vdouble AbstractTreeLikelihood::getLikelihoodPerSite ( ) const

virtualinherited

Get the likelihood for each site.

Returns

A vector with all likelihoods for each site.

Implements bpp::TreeLikelihoodInterface.

Definition at line 11 of file AbstractTreeLikelihood.cpp.

References bpp::TreeLikelihoodInterface::getLikelihoodForASite(), and bpp::AbstractTreeLikelihood::getNumberOfSites().

Referenced by bpp::AbstractDiscreteRatesAcrossSitesTreeLikelihood::getPosteriorProbabilitiesPerRate(), and bpp::AbstractDiscreteRatesAcrossSitesTreeLikelihood::getPosteriorRatePerSite().

getLikelihoodPerSite() [2/2]

virtual Vdouble bpp::TreeLikelihoodInterface::getLikelihoodPerSite ( ) const

pure virtualinherited

Get the likelihood for each site.

Returns

A vector with all likelihoods for each site.

Implemented in bpp::AbstractTreeLikelihood.

getLikelihoodPerSitePerRateClass()

VVdouble AbstractDiscreteRatesAcrossSitesTreeLikelihood::getLikelihoodPerSitePerRateClass ( ) const

virtualinherited

Get the likelihood for each site and each rate class.

Returns

A two-dimension vector with all likelihoods.

Implements bpp::DiscreteRatesAcrossSitesTreeLikelihoodInterface.

Definition at line 57 of file AbstractDiscreteRatesAcrossSitesTreeLikelihood.cpp.

References bpp::DiscreteRatesAcrossSitesTreeLikelihoodInterface::getLikelihoodForASiteForARateClass(), bpp::AbstractDiscreteRatesAcrossSitesTreeLikelihood::getNumberOfClasses(), and bpp::AbstractTreeLikelihood::getNumberOfSites().

Referenced by bpp::AbstractDiscreteRatesAcrossSitesTreeLikelihood::getPosteriorProbabilitiesPerRate(), bpp::AbstractDiscreteRatesAcrossSitesTreeLikelihood::getPosteriorRatePerSite(), bpp::AbstractDiscreteRatesAcrossSitesTreeLikelihood::getRateClassWithMaxPostProbPerSite(), and bpp::AbstractDiscreteRatesAcrossSitesTreeLikelihood::getRateWithMaxPostProbPerSite().

getLikelihoodPerSitePerRateClassPerState()

VVVdouble AbstractDiscreteRatesAcrossSitesTreeLikelihood::getLikelihoodPerSitePerRateClassPerState ( ) const

virtualinherited

Get the likelihood for each site and each rate class and each state.

Returns

A three-dimension vector with all likelihoods.

Implements bpp::DiscreteRatesAcrossSitesTreeLikelihoodInterface.

Definition at line 120 of file AbstractDiscreteRatesAcrossSitesTreeLikelihood.cpp.

References bpp::DiscreteRatesAcrossSitesTreeLikelihoodInterface::getLikelihoodForASiteForARateClassForAState(), bpp::AbstractDiscreteRatesAcrossSitesTreeLikelihood::getNumberOfClasses(), bpp::AbstractTreeLikelihood::getNumberOfSites(), and bpp::TreeLikelihoodInterface::getNumberOfStates().

getLikelihoodPerSitePerState() [1/2]

VVdouble AbstractTreeLikelihood::getLikelihoodPerSitePerState ( ) const

virtualinherited

Get the likelihood for each site and for each state.

Returns

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

Implements bpp::TreeLikelihoodInterface.

Definition at line 35 of file AbstractTreeLikelihood.cpp.

References bpp::TreeLikelihoodInterface::getLikelihoodForASiteForAState(), bpp::AbstractTreeLikelihood::getNumberOfSites(), and bpp::TreeLikelihoodInterface::getNumberOfStates().

getLikelihoodPerSitePerState() [2/2]

virtual VVdouble bpp::TreeLikelihoodInterface::getLikelihoodPerSitePerState ( ) const

pure virtualinherited

Get the likelihood for each site and for each state.

Returns

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

Implemented in bpp::AbstractTreeLikelihood.

getLogLikelihood()

double DRHomogeneousTreeLikelihood::getLogLikelihood ( ) const

overridevirtualinherited

Get the logarithm of the likelihood for the whole dataset.

Returns

The logarithm of the likelihood of the dataset.

Implements bpp::TreeLikelihoodInterface.

Definition at line 125 of file DRHomogeneousTreeLikelihood.cpp.

References bpp::DRHomogeneousTreeLikelihood::likelihoodData_, bpp::log(), and bpp::AbstractHomogeneousTreeLikelihood::nbDistinctSites_.

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

getLogLikelihoodForASite()

double DRHomogeneousTreeLikelihood::getLogLikelihoodForASite ( size_t  site ) const

overridevirtualinherited

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::TreeLikelihoodInterface.

Definition at line 153 of file DRHomogeneousTreeLikelihood.cpp.

References bpp::DRHomogeneousTreeLikelihood::likelihoodData_, and bpp::log().

getLogLikelihoodForASiteForARateClass()

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

overridevirtualinherited

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::DiscreteRatesAcrossSitesTreeLikelihoodInterface.

Definition at line 166 of file DRHomogeneousTreeLikelihood.cpp.

References bpp::DRHomogeneousTreeLikelihood::likelihoodData_, and bpp::log().

getLogLikelihoodForASiteForARateClassForAState()

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

overridevirtualinherited

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::DiscreteRatesAcrossSitesTreeLikelihoodInterface.

Definition at line 180 of file DRHomogeneousTreeLikelihood.cpp.

References bpp::DRHomogeneousTreeLikelihood::likelihoodData_, and bpp::log().

getLogLikelihoodForASiteForAState() [1/2]

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

virtualinherited

Get the logarithm of the likelihood for a site and for a state.

Parameters

site	The site index to analyse.
state	The state to consider.

Returns

The logarithm of the likelihood for site site and state state.

Implements bpp::TreeLikelihoodInterface.

Definition at line 88 of file AbstractDiscreteRatesAcrossSitesTreeLikelihood.cpp.

References bpp::DiscreteRatesAcrossSitesTreeLikelihoodInterface::getLikelihoodForASiteForARateClassForAState(), bpp::AbstractDiscreteRatesAcrossSitesTreeLikelihood::getNumberOfClasses(), bpp::log(), and bpp::AbstractDiscreteRatesAcrossSitesTreeLikelihood::rateDistribution_.

getLogLikelihoodForASiteForAState() [2/2]

virtual double bpp::TreeLikelihoodInterface::getLogLikelihoodForASiteForAState ( size_t  site, int  state  ) const

pure virtualinherited

Get the logarithm of the likelihood for a site and for a state.

Parameters

site	The site index to analyse.
state	The state to consider.

Returns

The logarithm of the likelihood for site site and state state.

Implemented in bpp::AbstractDiscreteRatesAcrossSitesTreeLikelihood.

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

getLogLikelihoodPerSite() [1/2]

Vdouble AbstractTreeLikelihood::getLogLikelihoodPerSite ( ) const

virtualinherited

Get the logarithm of the likelihood for each site.

Returns

A vector with all log likelihoods for each site.

Implements bpp::TreeLikelihoodInterface.

Definition at line 23 of file AbstractTreeLikelihood.cpp.

References bpp::TreeLikelihoodInterface::getLogLikelihoodForASite(), and bpp::AbstractTreeLikelihood::getNumberOfSites().

getLogLikelihoodPerSite() [2/2]

virtual Vdouble bpp::TreeLikelihoodInterface::getLogLikelihoodPerSite ( ) const

pure virtualinherited

Get the logarithm of the likelihood for each site.

Returns

A vector with all log likelihoods for each site.

Implemented in bpp::AbstractTreeLikelihood.

Referenced by bpp::PairedSiteLikelihoods::appendModel().

getLogLikelihoodPerSitePerRateClass()

VVdouble AbstractDiscreteRatesAcrossSitesTreeLikelihood::getLogLikelihoodPerSitePerRateClass ( ) const

virtualinherited

Get the logarithm of the likelihood for each site and each rate class.

Returns

A two-dimension vector with all log likelihoods: V[i][j] = likelihood of site i and rate class j.

Implements bpp::DiscreteRatesAcrossSitesTreeLikelihoodInterface.

Definition at line 102 of file AbstractDiscreteRatesAcrossSitesTreeLikelihood.cpp.

References bpp::DiscreteRatesAcrossSitesTreeLikelihoodInterface::getLogLikelihoodForASiteForARateClass(), bpp::AbstractDiscreteRatesAcrossSitesTreeLikelihood::getNumberOfClasses(), and bpp::AbstractTreeLikelihood::getNumberOfSites().

getLogLikelihoodPerSitePerRateClassPerState()

VVVdouble AbstractDiscreteRatesAcrossSitesTreeLikelihood::getLogLikelihoodPerSitePerRateClassPerState ( ) const

virtualinherited

Get the logarithm of the likelihood for each site and each rate class and each state.

Returns

A three-dimension vector with all log likelihoods: V[i][j][k} = likelihood of site i and rate class j and state k.

Implements bpp::DiscreteRatesAcrossSitesTreeLikelihoodInterface.

Definition at line 143 of file AbstractDiscreteRatesAcrossSitesTreeLikelihood.cpp.

References bpp::DiscreteRatesAcrossSitesTreeLikelihoodInterface::getLogLikelihoodForASiteForARateClassForAState(), bpp::AbstractDiscreteRatesAcrossSitesTreeLikelihood::getNumberOfClasses(), bpp::AbstractTreeLikelihood::getNumberOfSites(), and bpp::TreeLikelihoodInterface::getNumberOfStates().

getLogLikelihoodPerSitePerState() [1/2]

VVdouble AbstractTreeLikelihood::getLogLikelihoodPerSitePerState ( ) const

virtualinherited

Get the logarithm of the likelihood for each site and for each state.

Returns

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

Implements bpp::TreeLikelihoodInterface.

Definition at line 52 of file AbstractTreeLikelihood.cpp.

References bpp::TreeLikelihoodInterface::getLogLikelihoodForASiteForAState(), bpp::AbstractTreeLikelihood::getNumberOfSites(), and bpp::TreeLikelihoodInterface::getNumberOfStates().

getLogLikelihoodPerSitePerState() [2/2]

virtual VVdouble bpp::TreeLikelihoodInterface::getLogLikelihoodPerSitePerState ( ) const

pure virtualinherited

Get the logarithm of the likelihood for each site and for each state.

Returns

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

Implemented in bpp::AbstractTreeLikelihood.

getMaximumBranchLength()

virtual double bpp::AbstractHomogeneousTreeLikelihood::getMaximumBranchLength ( ) const

inlinevirtualinherited

Definition at line 239 of file AbstractHomogeneousTreeLikelihood.h.

References bpp::AbstractHomogeneousTreeLikelihood::maximumBrLen_.

getMinimumBranchLength()

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

inlinevirtualinherited

Definition at line 238 of file AbstractHomogeneousTreeLikelihood.h.

References bpp::AbstractHomogeneousTreeLikelihood::minimumBrLen_.

getModel() [1/4]

std::shared_ptr<TransitionModelInterface> bpp::AbstractHomogeneousTreeLikelihood::getModel ( )

inlinevirtualinherited

Returns

The substitution model attached to this instance.

Implements bpp::HomogeneousTreeLikelihood.

Definition at line 171 of file AbstractHomogeneousTreeLikelihood.h.

References bpp::AbstractHomogeneousTreeLikelihood::model_.

getModel() [2/4]

std::shared_ptr<const TransitionModelInterface> bpp::AbstractHomogeneousTreeLikelihood::getModel ( ) const

inlinevirtualinherited

Returns

The substitution model attached to this instance.

Implements bpp::HomogeneousTreeLikelihood.

Definition at line 168 of file AbstractHomogeneousTreeLikelihood.h.

References bpp::AbstractHomogeneousTreeLikelihood::model_.

getModel() [3/4]

std::shared_ptr<TransitionModelInterface> bpp::AbstractHomogeneousTreeLikelihood::getModel ( int  nodeId, size_t  siteIndex  )

inlineinherited

Definition at line 172 of file AbstractHomogeneousTreeLikelihood.h.

References bpp::AbstractHomogeneousTreeLikelihood::model_.

getModel() [4/4]

std::shared_ptr<const TransitionModelInterface> bpp::AbstractHomogeneousTreeLikelihood::getModel ( int  nodeId, size_t  siteIndex  ) const

inlineinherited

Definition at line 169 of file AbstractHomogeneousTreeLikelihood.h.

References bpp::AbstractHomogeneousTreeLikelihood::model_.

getModelForSite() [1/2]

std::shared_ptr<TransitionModelInterface> bpp::HomogeneousTreeLikelihood::getModelForSite ( int  nodeId, size_t  siteIndex  )

inlinevirtualinherited

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::TreeLikelihoodInterface.

Definition at line 35 of file HomogeneousTreeLikelihood.h.

References bpp::HomogeneousTreeLikelihood::getModel().

getModelForSite() [2/2]

std::shared_ptr<const TransitionModelInterface> bpp::HomogeneousTreeLikelihood::getModelForSite ( int  nodeId, size_t  siteIndex  ) const

inlinevirtualinherited

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.

Implements bpp::TreeLikelihoodInterface.

Definition at line 30 of file HomogeneousTreeLikelihood.h.

References bpp::HomogeneousTreeLikelihood::getModel().

getNewBranchModelIterator()

ConstBranchModelIterator* bpp::AbstractHomogeneousTreeLikelihood::getNewBranchModelIterator ( int  nodeId ) const

inlinevirtualinherited

Implements bpp::TreeLikelihoodInterface.

Definition at line 149 of file AbstractHomogeneousTreeLikelihood.h.

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

getNewSiteModelIterator()

ConstSiteModelIterator* bpp::AbstractHomogeneousTreeLikelihood::getNewSiteModelIterator ( size_t  siteIndex ) const

inlinevirtualinherited

Implements bpp::TreeLikelihoodInterface.

Definition at line 154 of file AbstractHomogeneousTreeLikelihood.h.

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

getNonDerivableParameters() [1/2]

ParameterList AbstractDiscreteRatesAcrossSitesTreeLikelihood::getNonDerivableParameters ( ) const

virtualinherited

All non derivable parameters.

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

Returns

A ParameterList.

Implements bpp::TreeLikelihoodInterface.

Definition at line 46 of file AbstractDiscreteRatesAcrossSitesTreeLikelihood.cpp.

References bpp::ParameterList::addParameters(), bpp::AbstractDiscreteRatesAcrossSitesTreeLikelihood::getRateDistributionParameters(), bpp::TreeLikelihoodInterface::getSubstitutionModelParameters(), and bpp::AbstractTreeLikelihood::initialized_.

getNonDerivableParameters() [2/2]

virtual ParameterList bpp::TreeLikelihoodInterface::getNonDerivableParameters ( ) const

pure virtualinherited

All non derivable parameters.

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

Returns

A ParameterList.

Implemented in bpp::AbstractDiscreteRatesAcrossSitesTreeLikelihood.

getNumberOfClasses()

size_t bpp::AbstractDiscreteRatesAcrossSitesTreeLikelihood::getNumberOfClasses ( ) const

inlinevirtualinherited

Get the number of classes.

Returns

The number of classes.

Implements bpp::DiscreteRatesAcrossSitesTreeLikelihoodInterface.

Definition at line 90 of file AbstractDiscreteRatesAcrossSitesTreeLikelihood.h.

References bpp::AbstractDiscreteRatesAcrossSitesTreeLikelihood::rateDistribution_.

Referenced by bpp::AbstractDiscreteRatesAcrossSitesTreeLikelihood::getLikelihoodForASiteForAState(), bpp::AbstractDiscreteRatesAcrossSitesTreeLikelihood::getLikelihoodPerSitePerRateClass(), bpp::AbstractDiscreteRatesAcrossSitesTreeLikelihood::getLikelihoodPerSitePerRateClassPerState(), bpp::AbstractDiscreteRatesAcrossSitesTreeLikelihood::getLogLikelihoodForASiteForAState(), bpp::AbstractDiscreteRatesAcrossSitesTreeLikelihood::getLogLikelihoodPerSitePerRateClass(), bpp::AbstractDiscreteRatesAcrossSitesTreeLikelihood::getLogLikelihoodPerSitePerRateClassPerState(), bpp::AbstractDiscreteRatesAcrossSitesTreeLikelihood::getPosteriorProbabilitiesPerRate(), bpp::AbstractDiscreteRatesAcrossSitesTreeLikelihood::getPosteriorRatePerSite(), and bpp::AbstractDiscreteRatesAcrossSitesTreeLikelihood::getTransitionProbabilities().

getNumberOfSites() [1/2]

size_t bpp::AbstractTreeLikelihood::getNumberOfSites ( ) const

inlinevirtualinherited

Get the number of sites in the dataset.

Returns

the number of sites in the dataset.

Implements bpp::TreeLikelihoodInterface.

Definition at line 268 of file AbstractTreeLikelihood.h.

References bpp::AbstractTreeLikelihood::data_.

Referenced by bpp::AbstractTreeLikelihood::getLikelihoodPerSite(), bpp::AbstractDiscreteRatesAcrossSitesTreeLikelihood::getLikelihoodPerSitePerRateClass(), bpp::AbstractDiscreteRatesAcrossSitesTreeLikelihood::getLikelihoodPerSitePerRateClassPerState(), bpp::AbstractTreeLikelihood::getLikelihoodPerSitePerState(), bpp::AbstractTreeLikelihood::getLogLikelihoodPerSite(), bpp::AbstractDiscreteRatesAcrossSitesTreeLikelihood::getLogLikelihoodPerSitePerRateClass(), bpp::AbstractDiscreteRatesAcrossSitesTreeLikelihood::getLogLikelihoodPerSitePerRateClassPerState(), bpp::AbstractTreeLikelihood::getLogLikelihoodPerSitePerState(), bpp::AbstractDiscreteRatesAcrossSitesTreeLikelihood::getPosteriorProbabilitiesPerRate(), bpp::AbstractDiscreteRatesAcrossSitesTreeLikelihood::getPosteriorRatePerSite(), bpp::AbstractDiscreteRatesAcrossSitesTreeLikelihood::getRateClassWithMaxPostProbPerSite(), and bpp::AbstractDiscreteRatesAcrossSitesTreeLikelihood::getRateWithMaxPostProbPerSite().

getNumberOfSites() [2/2]

virtual size_t bpp::TreeLikelihoodInterface::getNumberOfSites ( ) const

pure virtualinherited

Get the number of sites in the dataset.

Returns

the number of sites in the dataset.

Implemented in bpp::AbstractTreeLikelihood.

getNumberOfStates()

size_t bpp::AbstractHomogeneousTreeLikelihood::getNumberOfStates ( ) const

inlinevirtualinherited

Returns

the number of model states of the underlying Markov chain.

Implements bpp::TreeLikelihoodInterface.

Definition at line 126 of file AbstractHomogeneousTreeLikelihood.h.

References bpp::AbstractHomogeneousTreeLikelihood::model_.

getPosteriorProbabilitiesPerRate()

VVdouble AbstractDiscreteRatesAcrossSitesTreeLikelihood::getPosteriorProbabilitiesPerRate ( ) const

virtualinherited

Get the posterior probability for each site of belonging to a particular rate class.

Returns

A two-dimension vector with all posterior probabilities: V[i][j] = probability for site i of belonging to rate class j.

Implements bpp::DiscreteRatesAcrossSitesTreeLikelihoodInterface.

Definition at line 166 of file AbstractDiscreteRatesAcrossSitesTreeLikelihood.cpp.

References bpp::AbstractTreeLikelihood::getLikelihoodPerSite(), bpp::AbstractDiscreteRatesAcrossSitesTreeLikelihood::getLikelihoodPerSitePerRateClass(), bpp::AbstractDiscreteRatesAcrossSitesTreeLikelihood::getNumberOfClasses(), bpp::AbstractTreeLikelihood::getNumberOfSites(), and bpp::AbstractDiscreteRatesAcrossSitesTreeLikelihood::rateDistribution_.

getPosteriorRatePerSite()

Vdouble AbstractDiscreteRatesAcrossSitesTreeLikelihood::getPosteriorRatePerSite ( ) const

virtualinherited

Get the posterior rate, i.e. averaged over all classes and weighted with posterior probabilities, for each site.

Returns

A vector with all rates.

Implements bpp::DiscreteRatesAcrossSitesTreeLikelihoodInterface.

Definition at line 184 of file AbstractDiscreteRatesAcrossSitesTreeLikelihood.cpp.

References bpp::AbstractTreeLikelihood::getLikelihoodPerSite(), bpp::AbstractDiscreteRatesAcrossSitesTreeLikelihood::getLikelihoodPerSitePerRateClass(), bpp::AbstractDiscreteRatesAcrossSitesTreeLikelihood::getNumberOfClasses(), bpp::AbstractTreeLikelihood::getNumberOfSites(), and bpp::AbstractDiscreteRatesAcrossSitesTreeLikelihood::rateDistribution_.

getRateClassWithMaxPostProbPerSite()

vector< size_t > AbstractDiscreteRatesAcrossSitesTreeLikelihood::getRateClassWithMaxPostProbPerSite ( ) const

virtualinherited

Get the posterior rate class (the one with maximum posterior probability) for each site.

Returns

A vector with all rate classes indexes.

Implements bpp::DiscreteRatesAcrossSitesTreeLikelihoodInterface.

Definition at line 203 of file AbstractDiscreteRatesAcrossSitesTreeLikelihood.cpp.

References bpp::AbstractDiscreteRatesAcrossSitesTreeLikelihood::getLikelihoodPerSitePerRateClass(), and bpp::AbstractTreeLikelihood::getNumberOfSites().

getRateDistribution() [1/2]

std::shared_ptr<DiscreteDistributionInterface> bpp::AbstractDiscreteRatesAcrossSitesTreeLikelihood::getRateDistribution ( )

inlinevirtualinherited

Get the rate distribution used for the computation.

Returns

A pointer toward the rate distribution of this instance.

Implements bpp::DiscreteRatesAcrossSitesTreeLikelihoodInterface.

Definition at line 75 of file AbstractDiscreteRatesAcrossSitesTreeLikelihood.h.

References bpp::AbstractDiscreteRatesAcrossSitesTreeLikelihood::rateDistribution_.

getRateDistribution() [2/2]

std::shared_ptr<const DiscreteDistributionInterface> bpp::AbstractDiscreteRatesAcrossSitesTreeLikelihood::getRateDistribution ( ) const

inlinevirtualinherited

Get the rate distribution used for the computation.

Returns

A const pointer toward the rate distribution of this instance.

Implements bpp::DiscreteRatesAcrossSitesTreeLikelihoodInterface.

Definition at line 70 of file AbstractDiscreteRatesAcrossSitesTreeLikelihood.h.

References bpp::AbstractDiscreteRatesAcrossSitesTreeLikelihood::rateDistribution_.

getRateDistributionParameters()

ParameterList bpp::AbstractHomogeneousTreeLikelihood::getRateDistributionParameters ( ) const

inlinevirtualinherited

Get the parameters associated to the rate distribution.

Returns

A ParameterList object with all rate distribution parameters.

Reimplemented from bpp::AbstractDiscreteRatesAcrossSitesTreeLikelihood.

Definition at line 140 of file AbstractHomogeneousTreeLikelihood.h.

References bpp::AbstractDiscreteRatesAcrossSitesTreeLikelihood::getRateDistributionParameters().

Referenced by bpp::DRHomogeneousMixedTreeLikelihood::getFirstOrderDerivative(), bpp::RHomogeneousTreeLikelihood::getFirstOrderDerivative(), bpp::DRHomogeneousTreeLikelihood::getFirstOrderDerivative(), bpp::DRHomogeneousMixedTreeLikelihood::getSecondOrderDerivative(), bpp::RHomogeneousTreeLikelihood::getSecondOrderDerivative(), and bpp::DRHomogeneousTreeLikelihood::getSecondOrderDerivative().

getRateWithMaxPostProbPerSite()

Vdouble AbstractDiscreteRatesAcrossSitesTreeLikelihood::getRateWithMaxPostProbPerSite ( ) const

virtualinherited

Get the posterior rate (the one with maximum posterior probability) for each site.

Returns

A vector with all rate classes indexes.

Implements bpp::DiscreteRatesAcrossSitesTreeLikelihoodInterface.

Definition at line 217 of file AbstractDiscreteRatesAcrossSitesTreeLikelihood.cpp.

References bpp::AbstractDiscreteRatesAcrossSitesTreeLikelihood::getLikelihoodPerSitePerRateClass(), bpp::AbstractTreeLikelihood::getNumberOfSites(), and bpp::AbstractDiscreteRatesAcrossSitesTreeLikelihood::rateDistribution_.

getRootFrequencies()

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

inlinevirtualinherited

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::TreeLikelihoodInterface.

Definition at line 145 of file AbstractHomogeneousTreeLikelihood.h.

References bpp::AbstractHomogeneousTreeLikelihood::model_.

getSecondOrderDerivative() [1/2]

double DRHomogeneousTreeLikelihood::getSecondOrderDerivative ( const std::string &  variable ) const

overridevirtualinherited

Implements bpp::SecondOrderDerivable.

Definition at line 384 of file DRHomogeneousTreeLikelihood.cpp.

References bpp::Node::getId(), bpp::AbstractHomogeneousTreeLikelihood::getRateDistributionParameters(), bpp::AbstractHomogeneousTreeLikelihood::getSubstitutionModelParameters(), bpp::AbstractParametrizable::hasParameter(), bpp::DRHomogeneousTreeLikelihood::likelihoodData_, bpp::AbstractHomogeneousTreeLikelihood::nbDistinctSites_, bpp::AbstractHomogeneousTreeLikelihood::nodes_, and bpp::pow().

getSecondOrderDerivative() [2/2]

double bpp::DRHomogeneousTreeLikelihood::getSecondOrderDerivative ( const std::string &  variable1, const std::string &  variable2  ) const

inlineoverridevirtualinherited

Implements bpp::SecondOrderDerivable.

Definition at line 161 of file DRHomogeneousTreeLikelihood.h.

getSiteIndex()

size_t bpp::DRHomogeneousTreeLikelihood::getSiteIndex ( size_t  site ) const

inlineoverridevirtualinherited

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::TreeLikelihoodInterface.

Definition at line 112 of file DRHomogeneousTreeLikelihood.h.

References bpp::DRHomogeneousTreeLikelihood::likelihoodData_.

getSubstitutionModel() [1/2]

virtual std::shared_ptr<const SubstitutionModelInterface> bpp::AbstractHomogeneousTreeLikelihood::getSubstitutionModel ( ) const

inlinevirtualinherited

Get a SubstitutionModel pointer toward the model associated to this instance, if possible.

Performs a cast operation on the pointer. Return NULL if cast failed.

Returns

A SubstitutionModel pointer toward the model associated to this instance.

Implements bpp::HomogeneousTreeLikelihood.

Definition at line 183 of file AbstractHomogeneousTreeLikelihood.h.

References bpp::AbstractHomogeneousTreeLikelihood::model_.

getSubstitutionModel() [2/2]

virtual std::shared_ptr<const SubstitutionModelInterface> bpp::AbstractHomogeneousTreeLikelihood::getSubstitutionModel ( int  nodeId, size_t  siteIndex  ) const

inlinevirtualinherited

Get a SubstitutionModel pointer toward the model associated to this instance, if possible.

Performs a cast operation on the pointer. Return NULL if cast failed.

Returns

A SubstitutionModel pointer toward the model associated to this instance.

Parameters

nodeId	Id of the node
siteIndex	Position of the site

Implements bpp::HomogeneousTreeLikelihood.

Definition at line 197 of file AbstractHomogeneousTreeLikelihood.h.

References bpp::AbstractHomogeneousTreeLikelihood::model_.

getSubstitutionModelParameters()

ParameterList AbstractHomogeneousTreeLikelihood::getSubstitutionModelParameters ( ) const

virtualinherited

Get the parameters associated to substitution model(s).

Returns

A ParameterList.

Implements bpp::TreeLikelihoodInterface.

Definition at line 222 of file AbstractHomogeneousTreeLikelihood.cpp.

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

Referenced by bpp::DRHomogeneousMixedTreeLikelihood::getFirstOrderDerivative(), bpp::RHomogeneousTreeLikelihood::getFirstOrderDerivative(), bpp::DRHomogeneousTreeLikelihood::getFirstOrderDerivative(), bpp::DRHomogeneousMixedTreeLikelihood::getSecondOrderDerivative(), bpp::RHomogeneousTreeLikelihood::getSecondOrderDerivative(), and bpp::DRHomogeneousTreeLikelihood::getSecondOrderDerivative().

getTopologyValue()

double bpp::NNIHomogeneousTreeLikelihood::getTopologyValue ( ) const

inlineoverridevirtual

Get the current score of this NNISearchable object.

Returns

The current score of this instance.

Implements bpp::NNISearchable.

Definition at line 220 of file NNIHomogeneousTreeLikelihood.h.

References bpp::DRHomogeneousTreeLikelihood::getValue().

getTransitionProbabilities() [1/2]

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

virtualinherited

Retrieves all Pij(t) for a particular branch, defined by the upper node and site.

These intermediate results may be used by other methods.

Parameters

nodeId	The node defining the branch of interest.
siteIndex	The index of the alignment position.

See also

getSiteIndex

Returns

An array of dimension 2, where a[x][y] is the probability of substituting from x to y.

Implements bpp::TreeLikelihoodInterface.

Definition at line 275 of file AbstractDiscreteRatesAcrossSitesTreeLikelihood.cpp.

References bpp::AbstractDiscreteRatesAcrossSitesTreeLikelihood::getNumberOfClasses(), bpp::TreeLikelihoodInterface::getNumberOfStates(), bpp::DiscreteRatesAcrossSitesTreeLikelihoodInterface::getTransitionProbabilitiesPerRateClass(), and bpp::AbstractDiscreteRatesAcrossSitesTreeLikelihood::rateDistribution_.

getTransitionProbabilities() [2/2]

virtual VVdouble bpp::TreeLikelihoodInterface::getTransitionProbabilities ( int  nodeId, size_t  siteIndex  ) const

pure virtualinherited

Retrieves all Pij(t) for a particular branch, defined by the upper node and site.

These intermediate results may be used by other methods.

Parameters

nodeId	The node defining the branch of interest.
siteIndex	The index of the alignment position.

See also

getSiteIndex

Returns

An array of dimension 2, where a[x][y] is the probability of substituting from x to y.

Implemented in bpp::AbstractDiscreteRatesAcrossSitesTreeLikelihood.

Referenced by bpp::TreeLikelihoodTools::getAncestralFrequencies_().

getTransitionProbabilitiesPerRateClass()

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

inlinevirtualinherited

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::DiscreteRatesAcrossSitesTreeLikelihoodInterface.

Definition at line 147 of file AbstractHomogeneousTreeLikelihood.h.

References bpp::AbstractHomogeneousTreeLikelihood::pxy_.

getValue()

double DRHomogeneousTreeLikelihood::getValue ( ) const

overridevirtualinherited

Function and NNISearchable interface.

Implements bpp::SecondOrderDerivable.

Definition at line 233 of file DRHomogeneousTreeLikelihood.cpp.

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

Referenced by getTopologyValue(), and testNNI().

hasLikelihoodData() [1/2]

bool bpp::AbstractTreeLikelihood::hasLikelihoodData ( ) const

inlinevirtualinherited

Returns

True if the TreeLikelihood object has a LikelihoodData.

Implements bpp::TreeLikelihoodInterface.

Definition at line 261 of file AbstractTreeLikelihood.h.

References bpp::AbstractTreeLikelihood::data_.

Referenced by bpp::RNonHomogeneousMixedTreeLikelihood::init().

hasLikelihoodData() [2/2]

virtual bool bpp::TreeLikelihoodInterface::hasLikelihoodData ( ) const

pure virtualinherited

Returns

True if the TreeLikelihood object has a LikelihoodData.

Implemented in bpp::AbstractTreeLikelihood.

init_()

void DRHomogeneousTreeLikelihood::init_ ( )

privateinherited

Method called by constructors.

Definition at line 57 of file DRHomogeneousTreeLikelihood.cpp.

References bpp::DRHomogeneousTreeLikelihood::likelihoodData_, bpp::AbstractDiscreteRatesAcrossSitesTreeLikelihood::rateDistribution_, and bpp::AbstractTreeLikelihood::tree_.

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

initBranchLengthsParameters()

void AbstractHomogeneousTreeLikelihood::initBranchLengthsParameters ( bool  verbose = true )

virtualinherited

Definition at line 270 of file AbstractHomogeneousTreeLikelihood.cpp.

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

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

initialize()

void AbstractHomogeneousTreeLikelihood::initialize ( )

virtualinherited

Init the likelihood object.

This method is used to initialize all parameters. It is typically called after the constructor and the setData method. It contains virtual methods that can't be called in the constructor.

Exceptions

Exception

if something bad happened, for instance if no data are associated to the likelihood function.

Implements bpp::TreeLikelihoodInterface.

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

Definition at line 200 of file AbstractHomogeneousTreeLikelihood.cpp.

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

Referenced by bpp::DRHomogeneousMixedTreeLikelihood::initialize(), and bpp::RHomogeneousMixedTreeLikelihood::initialize().

initParameters()

void AbstractHomogeneousTreeLikelihood::initParameters ( )

virtualinherited

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

Definition at line 231 of file AbstractHomogeneousTreeLikelihood.cpp.

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

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

isInitialized() [1/2]

bool bpp::AbstractTreeLikelihood::isInitialized ( ) const

inlinevirtualinherited

Returns

'true' is the likelihood function has been initialized.

Implements bpp::TreeLikelihoodInterface.

Definition at line 275 of file AbstractTreeLikelihood.h.

References bpp::AbstractTreeLikelihood::initialized_.

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

isInitialized() [2/2]

virtual bool bpp::TreeLikelihoodInterface::isInitialized ( ) const

pure virtualinherited

Returns

'true' is the likelihood function has been initialized.

Implemented in bpp::AbstractTreeLikelihood.

likelihoodData() [1/2]

const DRASDRTreeLikelihoodData& bpp::DRHomogeneousTreeLikelihood::likelihoodData ( ) const

inlineoverridevirtualinherited

Returns

The underlying likelihood data structure.

Implements bpp::DRTreeLikelihoodInterface.

Definition at line 168 of file DRHomogeneousTreeLikelihood.h.

References bpp::DRHomogeneousTreeLikelihood::likelihoodData_.

likelihoodData() [2/2]

DRASDRTreeLikelihoodData& bpp::DRHomogeneousTreeLikelihood::likelihoodData ( )

inlineoverridevirtualinherited

Returns

The underlying likelihood data structure.

Implements bpp::DRTreeLikelihoodInterface.

Definition at line 167 of file DRHomogeneousTreeLikelihood.h.

References bpp::DRHomogeneousTreeLikelihood::likelihoodData_.

Referenced by NNIHomogeneousTreeLikelihood(), setData(), testNNI(), and topologyChangeTested().

operator=()

NNIHomogeneousTreeLikelihood & NNIHomogeneousTreeLikelihood::operator=

(

const NNIHomogeneousTreeLikelihood &

lik

)

Definition at line 151 of file NNIHomogeneousTreeLikelihood.cpp.

References brentOptimizer_, brLenNNIParams_, brLenNNIValues_, brLikFunction_, and bpp::DRHomogeneousTreeLikelihood::operator=().

rateDistribution() [1/2]

DiscreteDistributionInterface& bpp::AbstractDiscreteRatesAcrossSitesTreeLikelihood::rateDistribution ( )

inlinevirtualinherited

Get the rate distribution used for the computation.

Returns

A reference toward the rate distribution of this instance.

Implements bpp::DiscreteRatesAcrossSitesTreeLikelihoodInterface.

Definition at line 85 of file AbstractDiscreteRatesAcrossSitesTreeLikelihood.h.

References bpp::AbstractDiscreteRatesAcrossSitesTreeLikelihood::rateDistribution_.

rateDistribution() [2/2]

const DiscreteDistributionInterface& bpp::AbstractDiscreteRatesAcrossSitesTreeLikelihood::rateDistribution ( ) const

inlinevirtualinherited

Get the rate distribution used for the computation.

Returns

A const reference toward the rate distribution of this instance.

Implements bpp::DiscreteRatesAcrossSitesTreeLikelihoodInterface.

Definition at line 80 of file AbstractDiscreteRatesAcrossSitesTreeLikelihood.h.

References bpp::AbstractDiscreteRatesAcrossSitesTreeLikelihood::rateDistribution_.

resetLikelihoodArray()

void AbstractDiscreteRatesAcrossSitesTreeLikelihood::resetLikelihoodArray ( VVVdouble &  likelihoodArray )

staticinherited

Set all conditional likelihoods to 1.

Parameters

likelihoodArray

the likelihood array.

Definition at line 231 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(), bpp::DRNonHomogeneousTreeLikelihood::resetLikelihoodArrays(), and testNNI().

resetLikelihoodArrays()

void DRHomogeneousTreeLikelihood::resetLikelihoodArrays ( const Node *  node )

protectedvirtualinherited

Reimplemented in bpp::DRHomogeneousMixedTreeLikelihood.

Definition at line 417 of file DRHomogeneousTreeLikelihood.cpp.

References bpp::Node::getFather(), bpp::Node::getId(), bpp::Node::getNumberOfSons(), bpp::Node::getSon(), bpp::Node::hasFather(), bpp::DRHomogeneousTreeLikelihood::likelihoodData_, and bpp::AbstractDiscreteRatesAcrossSitesTreeLikelihood::resetLikelihoodArray().

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

setData()

void bpp::NNIHomogeneousTreeLikelihood::setData ( const AlignmentDataInterface &  sites )

inlineoverridevirtual

Set the dataset for which the likelihood must be evaluated.

Parameters

sites

The data set to use.

Reimplemented from bpp::DRHomogeneousTreeLikelihood.

Definition at line 201 of file NNIHomogeneousTreeLikelihood.h.

References brLikFunction_, bpp::DRHomogeneousTreeLikelihood::likelihoodData(), and bpp::DRHomogeneousTreeLikelihood::setData().

setMaximumBranchLength()

virtual void bpp::AbstractHomogeneousTreeLikelihood::setMaximumBranchLength ( double  maximum )

inlinevirtualinherited

Definition at line 229 of file AbstractHomogeneousTreeLikelihood.h.

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

setMinimumBranchLength()

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

inlinevirtualinherited

Definition at line 220 of file AbstractHomogeneousTreeLikelihood.h.

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

setModel()

void AbstractHomogeneousTreeLikelihood::setModel ( std::shared_ptr< TransitionModelInterface >  model )

virtualinherited

Returns

Set the substitution model for this instance.

Exceptions

Exception

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

Implements bpp::HomogeneousTreeLikelihood.

Definition at line 135 of file AbstractHomogeneousTreeLikelihood.cpp.

References bpp::AbstractHomogeneousTreeLikelihood::d2pxy_, bpp::AbstractTreeLikelihood::data_, bpp::AbstractHomogeneousTreeLikelihood::dpxy_, bpp::Node::getId(), bpp::AbstractHomogeneousTreeLikelihood::model_, bpp::AbstractHomogeneousTreeLikelihood::nbClasses_, bpp::AbstractHomogeneousTreeLikelihood::nbNodes_, bpp::AbstractHomogeneousTreeLikelihood::nbStates_, bpp::AbstractHomogeneousTreeLikelihood::nodes_, bpp::AbstractHomogeneousTreeLikelihood::pxy_, and bpp::TreeLikelihoodInterface::setData().

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

setParameters()

void DRHomogeneousTreeLikelihood::setParameters ( const ParameterList &  parameters )

overridevirtualinherited

Implements the Function interface.

Update the parameter list and call the fireParameterChanged() method.

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

Parameters

parameters

The parameter list to pass to the function.

Implements bpp::SecondOrderDerivable.

Definition at line 187 of file DRHomogeneousTreeLikelihood.cpp.

References bpp::AbstractParametrizable::setParametersValues().

testNNI()

double NNIHomogeneousTreeLikelihood::testNNI ( int  nodeId ) const

overridevirtual

Send the score of a NNI movement, without performing it.

This methods sends the score variation. This variation must be negative if the new point is better, i.e. the object is to be used with a minimizing optimization (for consistence with Optimizer objects).

Parameters

nodeId

The id of the node defining the NNI movement.

Returns

The score variation of the NNI.

Exceptions

NodeException

If the node does not define a valid NNI.

Implements bpp::NNISearchable.

Definition at line 167 of file NNIHomogeneousTreeLikelihood.cpp.

References bpp::ParameterList::addParameter(), brentOptimizer_, brLenNNIValues_, brLikFunction_, bpp::DRHomogeneousTreeLikelihood::computeLikelihoodFromArrays(), bpp::Node::getFather(), bpp::Node::getId(), bpp::DRASDRTreeLikelihoodNodeData::getLikelihoodArrayForNeighbor(), bpp::DRASDRTreeLikelihoodData::getNodeData(), bpp::TreeTemplateTools::getRemainingNeighbors(), bpp::Node::getSon(), bpp::Node::getSonPosition(), bpp::Parameter::getValue(), bpp::DRHomogeneousTreeLikelihood::getValue(), bpp::Node::hasFather(), bpp::DRHomogeneousTreeLikelihood::likelihoodData(), bpp::AbstractHomogeneousTreeLikelihood::model_, bpp::AbstractHomogeneousTreeLikelihood::nbClasses_, bpp::AbstractHomogeneousTreeLikelihood::nbDistinctSites_, bpp::AbstractHomogeneousTreeLikelihood::nbStates_, bpp::AbstractHomogeneousTreeLikelihood::nodes_, bpp::AbstractParametrizable::parameter(), bpp::AbstractHomogeneousTreeLikelihood::pxy_, bpp::AbstractDiscreteRatesAcrossSitesTreeLikelihood::rateDistribution_, bpp::AbstractDiscreteRatesAcrossSitesTreeLikelihood::resetLikelihoodArray(), bpp::AbstractHomogeneousTreeLikelihood::rootFreqs_, bpp::Parameter::setName(), bpp::TextTools::toString(), and bpp::AbstractTreeLikelihood::tree_.

topology()

const Tree& bpp::NNIHomogeneousTreeLikelihood::topology ( ) const

inlineoverridevirtual

Get the tree associated to this NNISearchable object.

Returns

The tree associated to this instance.

Implements bpp::NNISearchable.

Definition at line 218 of file NNIHomogeneousTreeLikelihood.h.

References bpp::AbstractTreeLikelihood::tree().

topologyChangePerformed()

virtual void bpp::TopologyListener::topologyChangePerformed ( const TopologyChangeEvent &  event )

inlinevirtualinherited

Notify a topology change event.

This method is to be invoked after one or several NNI are performed. It allows appropriate recomputations.

In most case, this is the same as topologyChangeTested() + topologyChangeSuccessful().

Parameters

event

The topology change event.

Definition at line 67 of file TopologySearch.h.

References bpp::TopologyListener::topologyChangeSuccessful(), and bpp::TopologyListener::topologyChangeTested().

topologyChangeSuccessful()

void bpp::NNIHomogeneousTreeLikelihood::topologyChangeSuccessful ( const TopologyChangeEvent &  event )

inlineoverridevirtual

Tell that a topology change is definitive.

This method is called after the topologyChangeTested() method.

Parameters

event

The topology change event.

Implements bpp::TopologyListener.

Definition at line 234 of file NNIHomogeneousTreeLikelihood.h.

References brLenNNIValues_.

topologyChangeTested()

void bpp::NNIHomogeneousTreeLikelihood::topologyChangeTested ( const TopologyChangeEvent &  event )

inlineoverridevirtual

Notify a topology change event.

Parameters

event

The topology change event.

Implements bpp::TopologyListener.

Definition at line 226 of file NNIHomogeneousTreeLikelihood.h.

References brLenNNIParams_, bpp::DRHomogeneousTreeLikelihood::fireParameterChanged(), bpp::DRHomogeneousTreeLikelihood::likelihoodData(), bpp::DRASDRTreeLikelihoodData::reInit(), and bpp::ParameterList::reset().

tree() [1/2]

const Tree& bpp::AbstractTreeLikelihood::tree ( ) const

inlinevirtualinherited

Get the tree (topology and branch lengths).

Returns

The tree of this TreeLikelihood object.

Implements bpp::TreeLikelihoodInterface.

Definition at line 269 of file AbstractTreeLikelihood.h.

References bpp::AbstractTreeLikelihood::tree_.

Referenced by bpp::AbstractHomogeneousTreeLikelihood::AbstractHomogeneousTreeLikelihood(), bpp::AbstractNonHomogeneousTreeLikelihood::AbstractNonHomogeneousTreeLikelihood(), bpp::DRHomogeneousMixedTreeLikelihood::DRHomogeneousMixedTreeLikelihood(), bpp::DRNonHomogeneousTreeLikelihood::DRNonHomogeneousTreeLikelihood(), bpp::RNonHomogeneousMixedTreeLikelihood::init(), bpp::AbstractNonHomogeneousTreeLikelihood::init_(), bpp::AbstractHomogeneousTreeLikelihood::init_(), bpp::RHomogeneousMixedTreeLikelihood::RHomogeneousMixedTreeLikelihood(), bpp::RNonHomogeneousMixedTreeLikelihood::RNonHomogeneousMixedTreeLikelihood(), bpp::RNonHomogeneousTreeLikelihood::RNonHomogeneousTreeLikelihood(), and topology().

tree() [2/2]

virtual const Tree& bpp::TreeLikelihoodInterface::tree ( ) const

pure virtualinherited

Get the tree (topology and branch lengths).

Returns

The tree of this TreeLikelihood object.

Implemented in bpp::AbstractTreeLikelihood.

Referenced by bpp::PairedSiteLikelihoods::appendModel(), bpp::TreeLikelihoodTools::getAncestralFrequencies(), bpp::TreeLikelihoodTools::getAncestralFrequencies_(), and bpp::DRTreeLikelihoodTools::getPosteriorProbabilitiesPerStatePerRate().

Member Data Documentation

brentOptimizer_

std::unique_ptr<BrentOneDimension> bpp::NNIHomogeneousTreeLikelihood::brentOptimizer_

protected

Optimizer used for testing NNI.

Definition at line 141 of file NNIHomogeneousTreeLikelihood.h.

Referenced by NNIHomogeneousTreeLikelihood(), operator=(), and testNNI().

brLenConstraint_

std::shared_ptr<ConstraintInterface> bpp::AbstractHomogeneousTreeLikelihood::brLenConstraint_

protectedinherited

Definition at line 82 of file AbstractHomogeneousTreeLikelihood.h.

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

brLenNNIParams_

ParameterList bpp::NNIHomogeneousTreeLikelihood::brLenNNIParams_

protected

Definition at line 148 of file NNIHomogeneousTreeLikelihood.h.

Referenced by doNNI(), NNIHomogeneousTreeLikelihood(), operator=(), and topologyChangeTested().

brLenNNIValues_

std::map<int, double> bpp::NNIHomogeneousTreeLikelihood::brLenNNIValues_

mutableprotected

Hash used for backing up branch lengths when testing NNIs.

Definition at line 146 of file NNIHomogeneousTreeLikelihood.h.

Referenced by doNNI(), NNIHomogeneousTreeLikelihood(), operator=(), testNNI(), and topologyChangeSuccessful().

brLenParameters_

ParameterList bpp::AbstractHomogeneousTreeLikelihood::brLenParameters_

protectedinherited

Definition at line 53 of file AbstractHomogeneousTreeLikelihood.h.

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

brLikFunction_

std::shared_ptr<BranchLikelihood> bpp::NNIHomogeneousTreeLikelihood::brLikFunction_

protected

Definition at line 136 of file NNIHomogeneousTreeLikelihood.h.

Referenced by NNIHomogeneousTreeLikelihood(), operator=(), setData(), and testNNI().

computeFirstOrderDerivatives_

bool bpp::AbstractTreeLikelihood::computeFirstOrderDerivatives_

protectedinherited

Definition at line 210 of file AbstractTreeLikelihood.h.

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

computeSecondOrderDerivatives_

bool bpp::AbstractTreeLikelihood::computeSecondOrderDerivatives_

protectedinherited

Definition at line 211 of file AbstractTreeLikelihood.h.

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

d2pxy_

std::map<int, VVVdouble> bpp::AbstractHomogeneousTreeLikelihood::d2pxy_

mutableprotectedinherited

Definition at line 59 of file AbstractHomogeneousTreeLikelihood.h.

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

data_

std::unique_ptr<const AlignmentDataInterface> bpp::AbstractTreeLikelihood::data_

protectedinherited

Definition at line 208 of file AbstractTreeLikelihood.h.

Referenced by bpp::AbstractTreeLikelihood::AbstractTreeLikelihood(), bpp::AbstractTreeLikelihood::data(), bpp::AbstractTreeLikelihood::getAlphabet(), bpp::AbstractTreeLikelihood::getNumberOfSites(), bpp::AbstractTreeLikelihood::hasLikelihoodData(), bpp::AbstractHomogeneousTreeLikelihood::initialize(), bpp::AbstractNonHomogeneousTreeLikelihood::initialize(), bpp::AbstractTreeLikelihood::operator=(), bpp::DRNonHomogeneousTreeLikelihood::setData(), bpp::RHomogeneousTreeLikelihood::setData(), bpp::RNonHomogeneousTreeLikelihood::setData(), bpp::DRHomogeneousTreeLikelihood::setData(), bpp::AbstractHomogeneousTreeLikelihood::setModel(), and bpp::AbstractNonHomogeneousTreeLikelihood::setSubstitutionModelSet().

dpxy_

std::map<int, VVVdouble> bpp::AbstractHomogeneousTreeLikelihood::dpxy_

mutableprotectedinherited

Definition at line 57 of file AbstractHomogeneousTreeLikelihood.h.

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

initialized_

bool bpp::AbstractTreeLikelihood::initialized_

protectedinherited

Definition at line 212 of file AbstractTreeLikelihood.h.

Referenced by bpp::AbstractHomogeneousTreeLikelihood::applyParameters(), bpp::AbstractNonHomogeneousTreeLikelihood::applyParameters(), bpp::AbstractHomogeneousTreeLikelihood::getBranchLengthsParameters(), bpp::AbstractNonHomogeneousTreeLikelihood::getBranchLengthsParameters(), bpp::AbstractDiscreteRatesAcrossSitesTreeLikelihood::getDerivableParameters(), bpp::AbstractDiscreteRatesAcrossSitesTreeLikelihood::getNonDerivableParameters(), bpp::AbstractDiscreteRatesAcrossSitesTreeLikelihood::getRateDistributionParameters(), bpp::AbstractHomogeneousTreeLikelihood::getSubstitutionModelParameters(), bpp::AbstractNonHomogeneousTreeLikelihood::getSubstitutionModelParameters(), bpp::AbstractHomogeneousTreeLikelihood::initialize(), bpp::AbstractTreeLikelihood::initialize(), bpp::AbstractNonHomogeneousTreeLikelihood::initialize(), bpp::AbstractTreeLikelihood::isInitialized(), bpp::AbstractTreeLikelihood::operator=(), bpp::DRNonHomogeneousTreeLikelihood::setData(), bpp::RHomogeneousTreeLikelihood::setData(), bpp::RNonHomogeneousTreeLikelihood::setData(), bpp::DRHomogeneousTreeLikelihood::setData(), and bpp::AbstractNonHomogeneousTreeLikelihood::setSubstitutionModelSet().

likelihoodData_

std::unique_ptr<DRASDRTreeLikelihoodData> bpp::DRHomogeneousTreeLikelihood::likelihoodData_

mutableprivateinherited

Definition at line 33 of file DRHomogeneousTreeLikelihood.h.

Referenced by bpp::DRHomogeneousTreeLikelihood::computeLikelihoodAtNode_(), bpp::DRHomogeneousTreeLikelihood::computeRootLikelihood(), bpp::DRHomogeneousTreeLikelihood::computeSubtreeLikelihoodPostfix(), bpp::DRHomogeneousTreeLikelihood::computeSubtreeLikelihoodPrefix(), bpp::DRHomogeneousTreeLikelihood::computeTreeD2LikelihoodAtNode(), bpp::DRHomogeneousTreeLikelihood::computeTreeDLikelihoodAtNode(), bpp::DRHomogeneousTreeLikelihood::displayLikelihood(), bpp::DRHomogeneousTreeLikelihood::DRHomogeneousTreeLikelihood(), bpp::DRHomogeneousMixedTreeLikelihood::getFirstOrderDerivative(), bpp::DRHomogeneousTreeLikelihood::getFirstOrderDerivative(), bpp::DRHomogeneousMixedTreeLikelihood::getLikelihood(), bpp::DRHomogeneousTreeLikelihood::getLikelihood(), bpp::DRHomogeneousTreeLikelihood::getLikelihoodForASite(), bpp::DRHomogeneousTreeLikelihood::getLikelihoodForASiteForARateClass(), bpp::DRHomogeneousTreeLikelihood::getLikelihoodForASiteForARateClassForAState(), bpp::DRHomogeneousMixedTreeLikelihood::getLogLikelihood(), bpp::DRHomogeneousTreeLikelihood::getLogLikelihood(), bpp::DRHomogeneousTreeLikelihood::getLogLikelihoodForASite(), bpp::DRHomogeneousTreeLikelihood::getLogLikelihoodForASiteForARateClass(), bpp::DRHomogeneousTreeLikelihood::getLogLikelihoodForASiteForARateClassForAState(), bpp::DRHomogeneousMixedTreeLikelihood::getSecondOrderDerivative(), bpp::DRHomogeneousTreeLikelihood::getSecondOrderDerivative(), bpp::DRHomogeneousTreeLikelihood::getSiteIndex(), bpp::DRHomogeneousTreeLikelihood::init_(), bpp::DRHomogeneousTreeLikelihood::likelihoodData(), bpp::DRHomogeneousTreeLikelihood::operator=(), bpp::DRHomogeneousTreeLikelihood::resetLikelihoodArrays(), and bpp::DRHomogeneousTreeLikelihood::setData().

maximumBrLen_

double bpp::AbstractHomogeneousTreeLikelihood::maximumBrLen_

protectedinherited

Definition at line 81 of file AbstractHomogeneousTreeLikelihood.h.

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

minimumBrLen_

double bpp::AbstractHomogeneousTreeLikelihood::minimumBrLen_

protectedinherited

Definition at line 80 of file AbstractHomogeneousTreeLikelihood.h.

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

minusLogLik_

double bpp::DRHomogeneousTreeLikelihood::minusLogLik_

protectedinherited

Definition at line 36 of file DRHomogeneousTreeLikelihood.h.

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

model_

std::shared_ptr<TransitionModelInterface> bpp::AbstractHomogeneousTreeLikelihood::model_

protectedinherited

Definition at line 52 of file AbstractHomogeneousTreeLikelihood.h.

Referenced by bpp::AbstractHomogeneousTreeLikelihood::applyParameters(), bpp::AbstractHomogeneousTreeLikelihood::computeAllTransitionProbabilities(), bpp::AbstractHomogeneousTreeLikelihood::computeTransitionProbabilitiesForNode(), bpp::DRHomogeneousMixedTreeLikelihood::DRHomogeneousMixedTreeLikelihood(), bpp::DRHomogeneousMixedTreeLikelihood::fireParameterChanged(), bpp::RHomogeneousMixedTreeLikelihood::fireParameterChanged(), bpp::RHomogeneousTreeLikelihood::fireParameterChanged(), bpp::DRHomogeneousTreeLikelihood::fireParameterChanged(), bpp::AbstractHomogeneousTreeLikelihood::getAlphabetStateAsChar(), bpp::AbstractHomogeneousTreeLikelihood::getAlphabetStateAsInt(), bpp::AbstractHomogeneousTreeLikelihood::getAlphabetStates(), bpp::AbstractHomogeneousTreeLikelihood::getModel(), bpp::AbstractHomogeneousTreeLikelihood::getNewBranchModelIterator(), bpp::AbstractHomogeneousTreeLikelihood::getNewSiteModelIterator(), bpp::AbstractHomogeneousTreeLikelihood::getNumberOfStates(), bpp::AbstractHomogeneousTreeLikelihood::getRootFrequencies(), bpp::AbstractHomogeneousTreeLikelihood::getSubstitutionModel(), bpp::AbstractHomogeneousTreeLikelihood::getSubstitutionModelParameters(), bpp::AbstractHomogeneousTreeLikelihood::initParameters(), bpp::AbstractHomogeneousTreeLikelihood::operator=(), bpp::RHomogeneousMixedTreeLikelihood::RHomogeneousMixedTreeLikelihood(), bpp::RHomogeneousTreeLikelihood::setData(), bpp::DRHomogeneousTreeLikelihood::setData(), bpp::AbstractHomogeneousTreeLikelihood::setModel(), and testNNI().

nbClasses_

size_t bpp::AbstractHomogeneousTreeLikelihood::nbClasses_

protectedinherited

Definition at line 74 of file AbstractHomogeneousTreeLikelihood.h.

Referenced by bpp::RHomogeneousTreeLikelihood::computeDownSubtreeD2Likelihood(), bpp::RHomogeneousTreeLikelihood::computeDownSubtreeDLikelihood(), bpp::DRHomogeneousMixedTreeLikelihood::computeLikelihoodAtNode_(), bpp::DRHomogeneousTreeLikelihood::computeLikelihoodAtNode_(), bpp::DRHomogeneousTreeLikelihood::computeRootLikelihood(), bpp::RHomogeneousTreeLikelihood::computeSubtreeLikelihood(), bpp::DRHomogeneousTreeLikelihood::computeSubtreeLikelihoodPostfix(), bpp::DRHomogeneousTreeLikelihood::computeSubtreeLikelihoodPrefix(), bpp::AbstractHomogeneousTreeLikelihood::computeTransitionProbabilitiesForNode(), bpp::RHomogeneousTreeLikelihood::computeTreeD2Likelihood(), bpp::DRHomogeneousTreeLikelihood::computeTreeD2LikelihoodAtNode(), bpp::RHomogeneousTreeLikelihood::computeTreeDLikelihood(), bpp::DRHomogeneousTreeLikelihood::computeTreeDLikelihoodAtNode(), bpp::RHomogeneousTreeLikelihood::getD2LikelihoodForASite(), bpp::RHomogeneousTreeLikelihood::getDLikelihoodForASite(), bpp::RHomogeneousTreeLikelihood::getLikelihoodForASite(), bpp::RHomogeneousTreeLikelihood::getLogLikelihoodForASite(), bpp::AbstractHomogeneousTreeLikelihood::init_(), bpp::AbstractHomogeneousTreeLikelihood::operator=(), bpp::AbstractHomogeneousTreeLikelihood::setModel(), and testNNI().

nbDistinctSites_

size_t bpp::AbstractHomogeneousTreeLikelihood::nbDistinctSites_

protectedinherited

Definition at line 73 of file AbstractHomogeneousTreeLikelihood.h.

Referenced by bpp::DRHomogeneousMixedTreeLikelihood::computeLikelihoodAtNode_(), bpp::DRHomogeneousTreeLikelihood::computeLikelihoodAtNode_(), bpp::DRHomogeneousTreeLikelihood::computeRootLikelihood(), bpp::DRHomogeneousTreeLikelihood::computeSubtreeLikelihoodPostfix(), bpp::DRHomogeneousTreeLikelihood::computeSubtreeLikelihoodPrefix(), bpp::DRHomogeneousTreeLikelihood::computeTreeD2LikelihoodAtNode(), bpp::DRHomogeneousTreeLikelihood::computeTreeDLikelihoodAtNode(), bpp::DRHomogeneousMixedTreeLikelihood::getFirstOrderDerivative(), bpp::DRHomogeneousTreeLikelihood::getFirstOrderDerivative(), bpp::DRHomogeneousMixedTreeLikelihood::getLikelihood(), bpp::DRHomogeneousTreeLikelihood::getLikelihood(), bpp::DRHomogeneousMixedTreeLikelihood::getLogLikelihood(), bpp::DRHomogeneousTreeLikelihood::getLogLikelihood(), bpp::AbstractHomogeneousTreeLikelihood::getNewBranchModelIterator(), bpp::DRHomogeneousMixedTreeLikelihood::getSecondOrderDerivative(), bpp::DRHomogeneousTreeLikelihood::getSecondOrderDerivative(), bpp::AbstractHomogeneousTreeLikelihood::operator=(), bpp::RHomogeneousTreeLikelihood::setData(), bpp::DRHomogeneousTreeLikelihood::setData(), and testNNI().

nbNodes_

size_t bpp::AbstractHomogeneousTreeLikelihood::nbNodes_

protectedinherited

Definition at line 76 of file AbstractHomogeneousTreeLikelihood.h.

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

nbSites_

size_t bpp::AbstractHomogeneousTreeLikelihood::nbSites_

protectedinherited

Definition at line 72 of file AbstractHomogeneousTreeLikelihood.h.

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

nbStates_

size_t bpp::AbstractHomogeneousTreeLikelihood::nbStates_

protectedinherited

Definition at line 75 of file AbstractHomogeneousTreeLikelihood.h.

Referenced by bpp::RHomogeneousTreeLikelihood::computeDownSubtreeD2Likelihood(), bpp::RHomogeneousTreeLikelihood::computeDownSubtreeDLikelihood(), bpp::DRHomogeneousMixedTreeLikelihood::computeLikelihoodAtNode_(), bpp::DRHomogeneousTreeLikelihood::computeLikelihoodAtNode_(), bpp::DRHomogeneousTreeLikelihood::computeRootLikelihood(), bpp::RHomogeneousTreeLikelihood::computeSubtreeLikelihood(), bpp::DRHomogeneousTreeLikelihood::computeSubtreeLikelihoodPostfix(), bpp::DRHomogeneousTreeLikelihood::computeSubtreeLikelihoodPrefix(), bpp::AbstractHomogeneousTreeLikelihood::computeTransitionProbabilitiesForNode(), bpp::RHomogeneousTreeLikelihood::computeTreeD2Likelihood(), bpp::DRHomogeneousTreeLikelihood::computeTreeD2LikelihoodAtNode(), bpp::RHomogeneousTreeLikelihood::computeTreeDLikelihood(), bpp::DRHomogeneousTreeLikelihood::computeTreeDLikelihoodAtNode(), bpp::RHomogeneousTreeLikelihood::getD2LikelihoodForASiteForARateClass(), bpp::RHomogeneousTreeLikelihood::getDLikelihoodForASiteForARateClass(), bpp::RHomogeneousTreeLikelihood::getLikelihoodForASiteForARateClass(), bpp::RHomogeneousTreeLikelihood::getLogLikelihoodForASiteForARateClass(), bpp::AbstractHomogeneousTreeLikelihood::operator=(), bpp::RHomogeneousTreeLikelihood::setData(), bpp::DRHomogeneousTreeLikelihood::setData(), bpp::AbstractHomogeneousTreeLikelihood::setModel(), and testNNI().

nodes_

std::vector<Node*> bpp::AbstractHomogeneousTreeLikelihood::nodes_

protectedinherited

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 69 of file AbstractHomogeneousTreeLikelihood.h.

Referenced by bpp::AbstractHomogeneousTreeLikelihood::AbstractHomogeneousTreeLikelihood(), bpp::AbstractHomogeneousTreeLikelihood::applyParameters(), bpp::AbstractHomogeneousTreeLikelihood::computeAllTransitionProbabilities(), bpp::RHomogeneousTreeLikelihood::computeTreeD2Likelihood(), bpp::DRHomogeneousTreeLikelihood::computeTreeD2Likelihoods(), bpp::RHomogeneousTreeLikelihood::computeTreeDLikelihood(), bpp::DRHomogeneousTreeLikelihood::computeTreeDLikelihoods(), doNNI(), bpp::RHomogeneousTreeLikelihood::fireParameterChanged(), bpp::DRHomogeneousTreeLikelihood::fireParameterChanged(), bpp::DRHomogeneousMixedTreeLikelihood::getFirstOrderDerivative(), bpp::DRHomogeneousTreeLikelihood::getFirstOrderDerivative(), bpp::DRHomogeneousMixedTreeLikelihood::getSecondOrderDerivative(), bpp::DRHomogeneousTreeLikelihood::getSecondOrderDerivative(), bpp::AbstractHomogeneousTreeLikelihood::init_(), bpp::AbstractHomogeneousTreeLikelihood::initBranchLengthsParameters(), bpp::AbstractHomogeneousTreeLikelihood::operator=(), bpp::AbstractHomogeneousTreeLikelihood::setModel(), and testNNI().

pxy_

std::map<int, VVVdouble> bpp::AbstractHomogeneousTreeLikelihood::pxy_

mutableprotectedinherited

Definition at line 55 of file AbstractHomogeneousTreeLikelihood.h.

Referenced by bpp::RHomogeneousTreeLikelihood::computeDownSubtreeD2Likelihood(), bpp::RHomogeneousTreeLikelihood::computeDownSubtreeDLikelihood(), bpp::DRHomogeneousTreeLikelihood::computeLikelihoodAtNode_(), bpp::DRHomogeneousTreeLikelihood::computeRootLikelihood(), bpp::RHomogeneousTreeLikelihood::computeSubtreeLikelihood(), bpp::DRHomogeneousTreeLikelihood::computeSubtreeLikelihoodPostfix(), bpp::DRHomogeneousTreeLikelihood::computeSubtreeLikelihoodPrefix(), bpp::AbstractHomogeneousTreeLikelihood::computeTransitionProbabilitiesForNode(), bpp::RHomogeneousTreeLikelihood::computeTreeD2Likelihood(), bpp::RHomogeneousTreeLikelihood::computeTreeDLikelihood(), bpp::AbstractHomogeneousTreeLikelihood::getTransitionProbabilitiesPerRateClass(), bpp::AbstractHomogeneousTreeLikelihood::operator=(), bpp::AbstractHomogeneousTreeLikelihood::setModel(), and testNNI().

rateDistribution_

std::shared_ptr<DiscreteDistributionInterface> bpp::AbstractDiscreteRatesAcrossSitesTreeLikelihood::rateDistribution_

protectedinherited

Definition at line 26 of file AbstractDiscreteRatesAcrossSitesTreeLikelihood.h.

Referenced by bpp::AbstractHomogeneousTreeLikelihood::applyParameters(), bpp::AbstractNonHomogeneousTreeLikelihood::applyParameters(), bpp::DRHomogeneousTreeLikelihood::computeRootLikelihood(), bpp::DRNonHomogeneousTreeLikelihood::computeRootLikelihood(), bpp::AbstractHomogeneousTreeLikelihood::computeTransitionProbabilitiesForNode(), bpp::AbstractNonHomogeneousTreeLikelihood::computeTransitionProbabilitiesForNode(), bpp::RNonHomogeneousMixedTreeLikelihood::computeTransitionProbabilitiesForNode(), bpp::DRHomogeneousTreeLikelihood::computeTreeD2LikelihoodAtNode(), bpp::DRNonHomogeneousTreeLikelihood::computeTreeD2LikelihoodAtNode(), bpp::DRHomogeneousTreeLikelihood::computeTreeDLikelihoodAtNode(), bpp::DRNonHomogeneousTreeLikelihood::computeTreeDLikelihoodAtNode(), bpp::DRNonHomogeneousTreeLikelihood::fireParameterChanged(), bpp::RHomogeneousTreeLikelihood::fireParameterChanged(), bpp::RNonHomogeneousMixedTreeLikelihood::fireParameterChanged(), bpp::RNonHomogeneousTreeLikelihood::fireParameterChanged(), bpp::DRHomogeneousTreeLikelihood::fireParameterChanged(), bpp::RHomogeneousTreeLikelihood::getD2LikelihoodForASite(), bpp::RNonHomogeneousTreeLikelihood::getD2LikelihoodForASite(), bpp::RHomogeneousTreeLikelihood::getDLikelihoodForASite(), bpp::RNonHomogeneousTreeLikelihood::getDLikelihoodForASite(), bpp::RHomogeneousTreeLikelihood::getLikelihoodForASite(), bpp::RNonHomogeneousTreeLikelihood::getLikelihoodForASite(), bpp::AbstractDiscreteRatesAcrossSitesTreeLikelihood::getLikelihoodForASiteForAState(), bpp::RHomogeneousTreeLikelihood::getLogLikelihoodForASite(), bpp::RNonHomogeneousTreeLikelihood::getLogLikelihoodForASite(), bpp::AbstractDiscreteRatesAcrossSitesTreeLikelihood::getLogLikelihoodForASiteForAState(), bpp::AbstractDiscreteRatesAcrossSitesTreeLikelihood::getNumberOfClasses(), bpp::AbstractDiscreteRatesAcrossSitesTreeLikelihood::getPosteriorProbabilitiesPerRate(), bpp::AbstractDiscreteRatesAcrossSitesTreeLikelihood::getPosteriorRatePerSite(), bpp::AbstractDiscreteRatesAcrossSitesTreeLikelihood::getRateDistribution(), bpp::AbstractDiscreteRatesAcrossSitesTreeLikelihood::getRateDistributionParameters(), bpp::AbstractDiscreteRatesAcrossSitesTreeLikelihood::getRateWithMaxPostProbPerSite(), bpp::DRNonHomogeneousTreeLikelihood::getSecondOrderDerivative(), bpp::AbstractDiscreteRatesAcrossSitesTreeLikelihood::getTransitionProbabilities(), bpp::RNonHomogeneousMixedTreeLikelihood::init(), bpp::DRHomogeneousTreeLikelihood::init_(), bpp::DRNonHomogeneousTreeLikelihood::init_(), bpp::RHomogeneousTreeLikelihood::init_(), bpp::RNonHomogeneousTreeLikelihood::init_(), bpp::AbstractNonHomogeneousTreeLikelihood::init_(), bpp::AbstractHomogeneousTreeLikelihood::init_(), bpp::AbstractHomogeneousTreeLikelihood::initParameters(), bpp::AbstractNonHomogeneousTreeLikelihood::initParameters(), bpp::AbstractDiscreteRatesAcrossSitesTreeLikelihood::operator=(), bpp::AbstractDiscreteRatesAcrossSitesTreeLikelihood::rateDistribution(), and testNNI().

rootFreqs_

std::vector<double> bpp::AbstractHomogeneousTreeLikelihood::rootFreqs_

protectedinherited

Definition at line 61 of file AbstractHomogeneousTreeLikelihood.h.

Referenced by bpp::AbstractHomogeneousTreeLikelihood::applyParameters(), bpp::AbstractHomogeneousTreeLikelihood::computeAllTransitionProbabilities(), bpp::DRHomogeneousTreeLikelihood::computeLikelihoodAtNode_(), bpp::DRHomogeneousTreeLikelihood::computeRootLikelihood(), bpp::DRHomogeneousTreeLikelihood::computeSubtreeLikelihoodPrefix(), bpp::RHomogeneousTreeLikelihood::fireParameterChanged(), bpp::RHomogeneousTreeLikelihood::getD2LikelihoodForASiteForARateClass(), bpp::RHomogeneousTreeLikelihood::getDLikelihoodForASiteForARateClass(), bpp::RHomogeneousTreeLikelihood::getLikelihoodForASiteForARateClass(), bpp::RHomogeneousTreeLikelihood::getLogLikelihoodForASiteForARateClass(), bpp::AbstractHomogeneousTreeLikelihood::operator=(), and testNNI().

tree_

std::shared_ptr< TreeTemplate<Node> > bpp::AbstractTreeLikelihood::tree_

mutableprotectedinherited

Definition at line 209 of file AbstractTreeLikelihood.h.

Referenced by bpp::AbstractHomogeneousTreeLikelihood::AbstractHomogeneousTreeLikelihood(), bpp::AbstractNonHomogeneousTreeLikelihood::AbstractNonHomogeneousTreeLikelihood(), bpp::AbstractTreeLikelihood::AbstractTreeLikelihood(), bpp::DRNonHomogeneousTreeLikelihood::computeLikelihoodAtNode(), bpp::DRHomogeneousTreeLikelihood::computeLikelihoodAtNode(), bpp::DRHomogeneousTreeLikelihood::computeRootLikelihood(), bpp::DRNonHomogeneousTreeLikelihood::computeRootLikelihood(), bpp::RNonHomogeneousMixedTreeLikelihood::computeTreeD2Likelihood(), bpp::RNonHomogeneousTreeLikelihood::computeTreeD2Likelihood(), bpp::RNonHomogeneousMixedTreeLikelihood::computeTreeDLikelihood(), bpp::RNonHomogeneousTreeLikelihood::computeTreeDLikelihood(), bpp::DRHomogeneousTreeLikelihood::computeTreeLikelihood(), bpp::DRNonHomogeneousTreeLikelihood::computeTreeLikelihood(), bpp::RHomogeneousTreeLikelihood::computeTreeLikelihood(), bpp::RNonHomogeneousTreeLikelihood::computeTreeLikelihood(), doNNI(), bpp::DRHomogeneousTreeLikelihood::DRHomogeneousTreeLikelihood(), bpp::DRNonHomogeneousTreeLikelihood::DRNonHomogeneousTreeLikelihood(), bpp::DRNonHomogeneousTreeLikelihood::fireParameterChanged(), bpp::RNonHomogeneousMixedTreeLikelihood::fireParameterChanged(), bpp::RNonHomogeneousTreeLikelihood::fireParameterChanged(), bpp::RHomogeneousTreeLikelihood::getD2LikelihoodForASiteForARateClass(), bpp::RNonHomogeneousTreeLikelihood::getD2LikelihoodForASiteForARateClass(), bpp::RHomogeneousTreeLikelihood::getDLikelihoodForASiteForARateClass(), bpp::RNonHomogeneousTreeLikelihood::getDLikelihoodForASiteForARateClass(), bpp::RHomogeneousTreeLikelihood::getLikelihoodForASiteForARateClass(), bpp::RNonHomogeneousTreeLikelihood::getLikelihoodForASiteForARateClass(), bpp::RHomogeneousTreeLikelihood::getLikelihoodForASiteForARateClassForAState(), bpp::RNonHomogeneousTreeLikelihood::getLikelihoodForASiteForARateClassForAState(), bpp::RHomogeneousTreeLikelihood::getLogLikelihoodForASiteForARateClass(), bpp::RNonHomogeneousTreeLikelihood::getLogLikelihoodForASiteForARateClass(), bpp::RHomogeneousTreeLikelihood::getLogLikelihoodForASiteForARateClassForAState(), bpp::RNonHomogeneousTreeLikelihood::getLogLikelihoodForASiteForARateClassForAState(), bpp::AbstractHomogeneousTreeLikelihood::getNewSiteModelIterator(), bpp::DRNonHomogeneousTreeLikelihood::getSecondOrderDerivative(), bpp::DRHomogeneousTreeLikelihood::init_(), bpp::DRNonHomogeneousTreeLikelihood::init_(), bpp::RHomogeneousTreeLikelihood::init_(), bpp::RNonHomogeneousTreeLikelihood::init_(), bpp::AbstractNonHomogeneousTreeLikelihood::init_(), bpp::AbstractHomogeneousTreeLikelihood::init_(), bpp::AbstractHomogeneousTreeLikelihood::operator=(), bpp::AbstractNonHomogeneousTreeLikelihood::operator=(), bpp::AbstractTreeLikelihood::operator=(), bpp::DRHomogeneousTreeLikelihood::operator=(), bpp::DRNonHomogeneousTreeLikelihood::operator=(), bpp::RHomogeneousTreeLikelihood::operator=(), bpp::RNonHomogeneousTreeLikelihood::operator=(), bpp::RHomogeneousTreeLikelihood::RHomogeneousTreeLikelihood(), bpp::RNonHomogeneousTreeLikelihood::RNonHomogeneousTreeLikelihood(), bpp::DRNonHomogeneousTreeLikelihood::setData(), bpp::RHomogeneousTreeLikelihood::setData(), bpp::RNonHomogeneousTreeLikelihood::setData(), bpp::DRHomogeneousTreeLikelihood::setData(), testNNI(), and bpp::AbstractTreeLikelihood::tree().

verbose_

bool bpp::AbstractHomogeneousTreeLikelihood::verbose_

protectedinherited

Definition at line 78 of file AbstractHomogeneousTreeLikelihood.h.

Referenced by bpp::AbstractHomogeneousTreeLikelihood::init_(), bpp::AbstractHomogeneousTreeLikelihood::operator=(), bpp::RHomogeneousTreeLikelihood::setData(), and bpp::DRHomogeneousTreeLikelihood::setData().

---

The documentation for this class was generated from the following files:

• Bpp/Phyl/Legacy/Likelihood/NNIHomogeneousTreeLikelihood.h
• Bpp/Phyl/Legacy/Likelihood/NNIHomogeneousTreeLikelihood.cpp